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
25170,SRR25661605,SRX21387413,SRS18627977,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD+/? 20 hpf CMs rep3,GSM7714404,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD+/? 20 hpf CMs rep3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS,GSM7714404,GSM7714404: hand2 FLD+/? 20 hpf CMs rep3; Danio rerio; RNA Seq,GSM7714404 r1,GSM7714404,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_het_3_R1.fastq.gz,fastq,2441736984.0,34141777.0,GSM7714404 r1,0:71.52,A:706186414;C:496261994;G:526176364;T:713112212;N:0,71,,,,706186414,496261994,526176364,713112212,0,SRX21387413,SRS18627977,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.9026,,0.15816,,0.76278,,0.44042,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25171,SRR25661606,SRX21387412,SRS18627976,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD+/? 20 hpf CMs rep2,GSM7714403,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD+/? 20 hpf CMs rep2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS,GSM7714403,GSM7714403: hand2 FLD+/? 20 hpf CMs rep2; Danio rerio; RNA Seq,GSM7714403 r1,GSM7714403,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_het_2_R1.fastq.gz,fastq,2185611269.0,30558084.0,GSM7714403 r1,0:71.52,A:612617675;C:458632518;G:474458738;T:639902338;N:0,71,,,,612617675,458632518,474458738,639902338,0,SRX21387412,SRS18627976,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90042,,0.14005,,0.75424,,0.44277,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25172,SRR25661607,SRX21387411,SRS18627975,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD+/? 20 hpf CMs rep1,GSM7714402,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD+/? 20 hpf CMs rep1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS,GSM7714402,GSM7714402: hand2 FLD+/? 20 hpf CMs rep1; Danio rerio; RNA Seq,GSM7714402 r1,GSM7714402,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_het_1_R1.fastq.gz,fastq,2291884894.0,32043147.0,GSM7714402 r1,0:71.52,A:635094975;C:489594953;G:499909828;T:667285138;N:0,71,,,,635094975,489594953,499909828,667285138,0,SRX21387411,SRS18627975,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90883,,0.14288,,0.75331,,0.44459,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25173,SRR25661608,SRX21387410,SRS18627974,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,WT 20 hpf CMs rep3,GSM7714401,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,WT 20 hpf CMs rep3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS,GSM7714401,GSM7714401: WT 20 hpf CMs rep3; Danio rerio; RNA Seq,GSM7714401 r1,GSM7714401,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_CMs_3_R1.fastq.gz,fastq,2268251602.0,31717610.0,GSM7714401 r1,0:71.51,A:637196241;C:477782543;G:497683941;T:655588877;N:0,71,,,,637196241,477782543,497683941,655588877,0,SRX21387410,SRS18627974,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90026,,0.13291,,0.78707,,0.40811,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25174,SRR25661609,SRX21387409,SRS18627973,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,WT 20 hpf CMs rep2,GSM7714400,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,WT 20 hpf CMs rep2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS,GSM7714400,GSM7714400: WT 20 hpf CMs rep2; Danio rerio; RNA Seq,GSM7714400 r1,GSM7714400,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_CMs_2_R1.fastq.gz,fastq,2195524610.0,30700033.0,GSM7714400 r1,0:71.52,A:615401741;C:462686936;G:481135567;T:636300366;N:0,71,,,,615401741,462686936,481135567,636300366,0,SRX21387409,SRS18627973,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90323,,0.1476,,0.78744,,0.41728,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25175,SRR25661610,SRX21387408,SRS18627972,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,WT 20 hpf CMs rep1,GSM7714399,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,WT 20 hpf CMs rep1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS,GSM7714399,GSM7714399: WT 20 hpf CMs rep1; Danio rerio; RNA Seq,GSM7714399 r1,GSM7714399,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_CMs_1_R1.fastq.gz,fastq,2258160684.0,31576661.0,GSM7714399 r1,0:71.51,A:641254288;C:471580136;G:491501482;T:653824778;N:0,71,,,,641254288,471580136,491501482,653824778,0,SRX21387408,SRS18627972,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.9,,0.13993,,0.78445,,0.40575,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25176,SRR25661611,SRX21387407,SRS18627971,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 OE 20 hpf CMs rep3,GSM7714398,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 OE 20 hpf CMs rep3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS,GSM7714398,GSM7714398: hand2 OE 20 hpf CMs rep3; Danio rerio; RNA Seq,GSM7714398 r1,GSM7714398,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_OE_CMs_3_R1.fastq.gz,fastq,1886569909.0,26380170.0,GSM7714398 r1,0:71.51,A:534874421;C:392168718;G:411533838;T:547992932;N:0,71,,,,534874421,392168718,411533838,547992932,0,SRX21387407,SRS18627971,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.89968,,0.14763,,0.77881,,0.42601,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25177,SRR25661612,SRX21387406,SRS18627970,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 OE 20 hpf CMs rep2,GSM7714397,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 OE 20 hpf CMs rep2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS,GSM7714397,GSM7714397: hand2 OE 20 hpf CMs rep2; Danio rerio; RNA Seq,GSM7714397 r1,GSM7714397,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_OE_CMs_2_R1.fastq.gz,fastq,2197151812.0,30722639.0,GSM7714397 r1,0:71.52,A:617116635;C:461951919;G:481371246;T:636712012;N:0,71,,,,617116635,461951919,481371246,636712012,0,SRX21387406,SRS18627970,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90877,,0.14744,,0.77191,,0.42845,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25178,SRR25661613,SRX21387405,SRS18627969,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 OE 20 hpf CMs rep1,GSM7714396,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 OE 20 hpf CMs rep1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS,GSM7714396,GSM7714396: hand2 OE 20 hpf CMs rep1; Danio rerio; RNA Seq,GSM7714396 r1,GSM7714396,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_OE_CMs_1_R1.fastq.gz,fastq,1773398936.0,24797998.0,GSM7714396 r1,0:71.51,A:495618212;C:375438077;G:390377060;T:511965587;N:0,71,,,,495618212,375438077,390377060,511965587,0,SRX21387405,SRS18627969,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90769,,0.1387,,0.7768,,0.42096,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25179,SRR25661614,SRX21387404,SRS18627968,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD /  20 hpf CMs rep3,GSM7714395,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD /  20 hpf CMs rep3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS,GSM7714395,GSM7714395: hand2 FLD /  20 hpf CMs rep3; Danio rerio; RNA Seq,GSM7714395 r1,GSM7714395,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_Mut_3_R1.fastq.gz,fastq,2179400259.0,30471965.0,GSM7714395 r1,0:71.52,A:600555691;C:468535203;G:483122661;T:627186704;N:0,71,,,,600555691,468535203,483122661,627186704,0,SRX21387404,SRS18627968,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.91581,,0.12256,,0.75209,,0.43413,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25180,SRR25661615,SRX21387403,SRS18627967,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD /  20 hpf CMs rep2,GSM7714394,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD /  20 hpf CMs rep2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS,GSM7714394,GSM7714394: hand2 FLD /  20 hpf CMs rep2; Danio rerio; RNA Seq,GSM7714394 r1,GSM7714394,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_Mut_2_R1.fastq.gz,fastq,2340991168.0,32733068.0,GSM7714394 r1,0:71.52,A:647423337;C:500120073;G:514803152;T:678644606;N:0,71,,,,647423337,500120073,514803152,678644606,0,SRX21387403,SRS18627967,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.91231,,0.12561,,0.75118,,0.44445,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25181,SRR25661616,SRX21387402,SRS18627966,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD /  20 hpf CMs rep1,GSM7714393,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD /  20 hpf CMs rep1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS,GSM7714393,GSM7714393: hand2 FLD /  20 hpf CMs rep1; Danio rerio; RNA Seq,GSM7714393 r1,GSM7714393,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_Mut_1_R1.fastq.gz,fastq,2727863036.0,38140997.0,GSM7714393 r1,0:71.52,A:760867462;C:577539041;G:596986102;T:792470431;N:0,71,,,,760867462,577539041,596986102,792470431,0,SRX21387402,SRS18627966,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.91175,,0.1342,,0.75282,,0.44063,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
48416,SRR7252518,SRX4157244,SRS3369695,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group3 Library3,GSM3172818,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group3 Library3,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172818,GSM3172818: Group3 Library3; Danio rerio; RNA Seq,GSM3172818,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172818,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group3_Library3_R1.fastq Group3_Library3_R2.fastq,fastq fastq,10582682434.0,52389517.0,GSM3172818 r1,0:101 1:101,A:2920935491;C:2280838256;G:2373423629;T:3004636928;N:2848130,101,101,,,2920935491,2280838256,2373423629,3004636928,2848130,SRX4157244,SRS3369695,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.82243,0.81602,0.34973,0.34907,0.7959,0.80415,0.58533,0.57989,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48417,SRR7252517,SRX4157243,SRS3369694,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group3 Library2,GSM3172817,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group3 Library2,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172817,GSM3172817: Group3 Library2; Danio rerio; RNA Seq,GSM3172817,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172817,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group3_Library2_R2.fastq Group3_Library2_R1.fastq,fastq fastq,8398868312.0,41578556.0,GSM3172817 r1,0:101 1:101,A:2365832903;C:1714320588;G:1799780549;T:2459288921;N:59645351,101,101,,,2365832903,1714320588,1799780549,2459288921,59645351,SRX4157243,SRS3369694,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.80215,0.80055,0.29918,0.29795,0.78139,0.78567,0.53014,0.5304,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48418,SRR7252516,SRX4157242,SRS3369693,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group3 Library1,GSM3172816,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group3 Library1,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172816,GSM3172816: Group3 Library1; Danio rerio; RNA Seq,GSM3172816,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172816,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group3_Library1_R2.fastq Group3_Library1_R1.fastq,fastq fastq,8784708916.0,43488658.0,GSM3172816 r1,0:101 1:101,A:2237850943;C:1944771284;G:2092315228;T:2411084639;N:98686822,101,101,,,2237850943,1944771284,2092315228,2411084639,98686822,SRX4157242,SRS3369693,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.83019,0.80927,0.27745,0.27973,0.78835,0.80835,0.63272,0.63323,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48419,SRR7252515,SRX4157241,SRS3369740,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group2 Library3,GSM3172815,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group2 Library3,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172815,GSM3172815: Group2 Library3; Danio rerio; RNA Seq,GSM3172815,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172815,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group2_Library3_R1.fastq Group2_Library3_R2.fastq,fastq fastq,7224792398.0,35766299.0,GSM3172815 r1,0:101 1:101,A:1966971879;C:1598533948;G:1648392712;T:2008955757;N:1938102,101,101,,,1966971879,1598533948,1648392712,2008955757,1938102,SRX4157241,SRS3369740,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.83962,0.8342,0.30832,0.30786,0.76455,0.77315,0.60778,0.60922,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48420,SRR7252514,SRX4157240,SRS3369692,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group2 Library2,GSM3172814,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group2 Library2,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172814,GSM3172814: Group2 Library2; Danio rerio; RNA Seq,GSM3172814,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172814,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group2_Library2_R1.fastq Group2_Library2_R2.fastq,fastq fastq,7203903174.0,35662887.0,GSM3172814 r1,0:101 1:101,A:2001767256;C:1497645415;G:1580912101;T:2072372149;N:51206253,101,101,,,2001767256,1497645415,1580912101,2072372149,51206253,SRX4157240,SRS3369692,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.77898,0.77807,0.34363,0.34395,0.79034,0.79375,0.5816,0.58087,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48421,SRR7252513,SRX4157239,SRS3369691,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group2 Library1,GSM3172813,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group2 Library1,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172813,GSM3172813: Group2 Library1; Danio rerio; RNA Seq,GSM3172813,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172813,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group2_Library1_R1.fastq Group2_Library1_R2.fastq,fastq fastq,8442759478.0,41795839.0,GSM3172813 r1,0:101 1:101,A:2196493743;C:1822028333;G:1974061919;T:2376981823;N:73193660,101,101,,,2196493743,1822028333,1974061919,2376981823,73193660,SRX4157239,SRS3369691,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.82021,0.79025,0.30166,0.29983,0.79482,0.81481,0.63103,0.63063,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48422,SRR7252512,SRX4157238,SRS3369690,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group1 Library3,GSM3172812,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group1 Library3,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172812,GSM3172812: Group1 Library3; Danio rerio; RNA Seq,GSM3172812,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172812,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group1_Library3_R1.fastq Group1_Library3_R2.fastq,fastq fastq,8304010526.0,41108963.0,GSM3172812 r1,0:101 1:101,A:2312592520;C:1775301647;G:1843137604;T:2370733357;N:2245398,101,101,,,2312592520,1775301647,1843137604,2370733357,2245398,SRX4157238,SRS3369690,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.79607,0.78867,0.28146,0.28007,0.8047,0.81432,0.58876,0.58873,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48423,SRR7252511,SRX4157237,SRS3369689,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group1 Library2,GSM3172811,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group1 Library2,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172811,GSM3172811: Group1 Library2; Danio rerio; RNA Seq,GSM3172811,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172811,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group1_Library2_R1.fastq Group1_Library2_R2.fastq,fastq fastq,8404855794.0,41608197.0,GSM3172811 r1,0:101 1:101,A:2332624405;C:1762786007;G:1853386011;T:2396361483;N:59697888,101,101,,,2332624405,1762786007,1853386011,2396361483,59697888,SRX4157237,SRS3369689,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.80769,0.78126,0.31373,0.30654,0.7781,0.78644,0.53559,0.54605,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48424,SRR7252510,SRX4157236,SRS3369688,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group1 Library1,GSM3172810,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group1 Library1,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172810,GSM3172810: Group1 Library1; Danio rerio; RNA Seq,GSM3172810,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172810,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group1_Library1_R1.fastq Group1_Library1_R2.fastq,fastq fastq,8075069988.0,39975594.0,GSM3172810 r1,0:101 1:101,A:2111117991;C:1746554669;G:1884216047;T:2242387738;N:90793543,101,101,,,2111117991,1746554669,1884216047,2242387738,90793543,SRX4157236,SRS3369688,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.80138,0.79326,0.29563,0.30562,0.80304,0.81854,0.5754,0.61905,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
55747,SRR10753218,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN707-S517=Aug1_Cell_49.fastq.gz run1696_lane2_read1_indexN707-S517=Aug1_Cell_49.fastq.gz,fastq fastq,283120950.0,1887473.0,GSM4230287 r1,0:75 1:75,A:78921390;C:62364350;G:62670695;T:79125765;N:38750,75,75,,,78921390,62364350,62670695,79125765,38750,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90632,0.92036,0.16158,0.16744,0.93332,0.93389,0.4857,0.48751,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55748,SRR10753219,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN709-S502=Aug1_Cell_58.fastq.gz run1696_lane2_read1_indexN709-S502=Aug1_Cell_58.fastq.gz,fastq fastq,245846550.0,1638977.0,GSM4230287 r10,0:75 1:75,A:67896939;C:54764431;G:55135813;T:68016031;N:33336,75,75,,,67896939,54764431,55135813,68016031,33336,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90267,0.90773,0.18676,0.18997,0.92983,0.92971,0.49203,0.49454,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55749,SRR10753220,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN710-S503=Aug1_Cell_59.fastq.gz run1696_lane2_read1_indexN710-S503=Aug1_Cell_59.fastq.gz,fastq fastq,254226450.0,1694843.0,GSM4230287 r11,0:75 1:75,A:72181308;C:54619189;G:54984718;T:72405980;N:35255,75,75,,,72181308,54619189,54984718,72405980,35255,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89184,0.89943,0.33071,0.3348,0.90538,0.90514,0.54519,0.54232,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55750,SRR10753221,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN711-S504=Aug1_Cell_60.fastq.gz run1696_lane2_read2_indexN711-S504=Aug1_Cell_60.fastq.gz,fastq fastq,272723400.0,1818156.0,GSM4230287 r12,0:75 1:75,A:75891977;C:60178887;G:60639000;T:75975500;N:38036,75,75,,,75891977,60178887,60639000,75975500,38036,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91617,0.92262,0.19662,0.20134,0.93072,0.9307,0.43264,0.43459,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55751,SRR10753222,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN712-S505=Aug1_Cell_61.fastq.gz run1696_lane2_read1_indexN712-S505=Aug1_Cell_61.fastq.gz,fastq fastq,328643250.0,2190955.0,GSM4230287 r13,0:75 1:75,A:91428860;C:72391345;G:72874053;T:91904041;N:44951,75,75,,,91428860,72391345,72874053,91904041,44951,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90728,0.91292,0.20245,0.20556,0.91701,0.91664,0.47925,0.47785,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55752,SRR10753223,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S506=Aug1_Cell_62.fastq.gz run1696_lane2_read2_indexN701-S506=Aug1_Cell_62.fastq.gz,fastq fastq,393051600.0,2620344.0,GSM4230287 r14,0:75 1:75,A:107520133;C:88489033;G:89202131;T:107788164;N:52139,75,75,,,107520133,88489033,89202131,107788164,52139,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91538,0.92003,0.14754,0.14967,0.89438,0.89572,0.48906,0.46829,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55753,SRR10753224,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S507=Aug1_Cell_63.fastq.gz run1696_lane2_read2_indexN702-S507=Aug1_Cell_63.fastq.gz,fastq fastq,266633850.0,1777559.0,GSM4230287 r15,0:75 1:75,A:75310904;C:57522159;G:58016352;T:75748192;N:36243,75,75,,,75310904,57522159,58016352,75748192,36243,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.8963,0.91004,0.26603,0.27276,0.92064,0.91993,0.49301,0.49362,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55754,SRR10753225,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S508=Aug1_Cell_64.fastq.gz run1696_lane2_read2_indexN703-S508=Aug1_Cell_64.fastq.gz,fastq fastq,320260050.0,2135067.0,GSM4230287 r16,0:75 1:75,A:88326766;C:70952312;G:71719762;T:89217755;N:43455,75,75,,,88326766,70952312,71719762,89217755,43455,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90631,0.91303,0.17305,0.1758,0.91226,0.91194,0.4751,0.47508,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55755,SRR10753226,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN709-S517=Aug1_Cell_65.fastq.gz run1696_lane2_read1_indexN709-S517=Aug1_Cell_65.fastq.gz,fastq fastq,237092850.0,1580619.0,GSM4230287 r17,0:75 1:75,A:65593919;C:52797142;G:53078356;T:65591887;N:31546,75,75,,,65593919,52797142,53078356,65591887,31546,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.9084,0.91253,0.16047,0.16296,0.91291,0.91232,0.47821,0.48265,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55756,SRR10753227,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN710-S502=Aug1_Cell_66.fastq.gz run1696_lane2_read2_indexN710-S502=Aug1_Cell_66.fastq.gz,fastq fastq,203466600.0,1356444.0,GSM4230287 r18,0:75 1:75,A:57338640;C:43614133;G:44244871;T:58241187;N:27769,75,75,,,57338640,43614133,44244871,58241187,27769,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.88694,0.89395,0.35775,0.36017,0.93371,0.93428,0.64977,0.64812,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55757,SRR10753228,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN711-S503=Aug1_Cell_67.fastq.gz run1696_lane2_read2_indexN711-S503=Aug1_Cell_67.fastq.gz,fastq fastq,382760100.0,2551734.0,GSM4230287 r19,0:75 1:75,A:104074844;C:86846190;G:87465046;T:104321801;N:52219,75,75,,,104074844,86846190,87465046,104321801,52219,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.92294,0.92788,0.14352,0.14599,0.91845,0.91782,0.48227,0.48103,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55758,SRR10753229,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN708-S502=Aug1_Cell_50.fastq.gz run1696_lane2_read2_indexN708-S502=Aug1_Cell_50.fastq.gz,fastq fastq,267098700.0,1780658.0,GSM4230287 r2,0:75 1:75,A:74382570;C:58775515;G:59120917;T:74783242;N:36456,75,75,,,74382570,58775515,59120917,74783242,36456,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90724,0.91983,0.2402,0.24535,0.92547,0.92533,0.45641,0.4586,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55759,SRR10753230,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN712-S504=Aug1_Cell_68.fastq.gz run1696_lane2_read2_indexN712-S504=Aug1_Cell_68.fastq.gz,fastq fastq,318756750.0,2125045.0,GSM4230287 r20,0:75 1:75,A:87025537;C:72058246;G:72667582;T:86962614;N:42771,75,75,,,87025537,72058246,72667582,86962614,42771,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91149,0.91879,0.14134,0.14484,0.9181,0.91839,0.48713,0.48686,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55760,SRR10753231,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S505=Aug1_Cell_69.fastq.gz run1696_lane2_read2_indexN701-S505=Aug1_Cell_69.fastq.gz,fastq fastq,284858550.0,1899057.0,GSM4230287 r21,0:75 1:75,A:78978323;C:63093139;G:63404944;T:79343904;N:38240,75,75,,,78978323,63093139,63404944,79343904,38240,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91426,0.92025,0.1863,0.18952,0.92855,0.92849,0.50311,0.50162,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55761,SRR10753232,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S506=Aug1_Cell_70.fastq.gz run1696_lane2_read2_indexN702-S506=Aug1_Cell_70.fastq.gz,fastq fastq,284898300.0,1899322.0,GSM4230287 r22,0:75 1:75,A:78397302;C:63504322;G:64181815;T:78775032;N:39829,75,75,,,78397302,63504322,64181815,78775032,39829,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90463,0.9098,0.13564,0.137,0.90382,0.90461,0.48397,0.4914,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55762,SRR10753233,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S507=Aug1_Cell_71.fastq.gz run1696_lane2_read2_indexN703-S507=Aug1_Cell_71.fastq.gz,fastq fastq,320753850.0,2138359.0,GSM4230287 r23,0:75 1:75,A:88975252;C:70589715;G:71455216;T:89691991;N:41676,75,75,,,88975252,70589715,71455216,89691991,41676,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.87801,0.88372,0.22781,0.23132,0.9036,0.90408,0.47968,0.48892,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55763,SRR10753234,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN704-S508=Aug1_Cell_72.fastq.gz run1696_lane2_read2_indexN704-S508=Aug1_Cell_72.fastq.gz,fastq fastq,299361600.0,1995744.0,GSM4230287 r24,0:75 1:75,A:79430814;C:70183806;G:70603054;T:79102903;N:41023,75,75,,,79430814,70183806,70603054,79102903,41023,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90697,0.91051,0.13467,0.13564,0.92669,0.92691,0.44358,0.43646,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55764,SRR10753235,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN710-S517=Aug1_Cell_73.fastq.gz run1696_lane2_read2_indexN710-S517=Aug1_Cell_73.fastq.gz,fastq fastq,177953400.0,1186356.0,GSM4230287 r25,0:75 1:75,A:50000069;C:38723482;G:38933711;T:50273254;N:22884,75,75,,,50000069,38723482,38933711,50273254,22884,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90193,0.91597,0.18328,0.18867,0.95063,0.95028,0.47314,0.47044,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55765,SRR10753236,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN711-S502=Aug1_Cell_74.fastq.gz run1696_lane2_read2_indexN711-S502=Aug1_Cell_74.fastq.gz,fastq fastq,279180300.0,1861202.0,GSM4230287 r26,0:75 1:75,A:78643117;C:60355928;G:60826366;T:79317071;N:37818,75,75,,,78643117,60355928,60826366,79317071,37818,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.9052,0.90984,0.27142,0.27375,0.96867,0.96865,0.51907,0.52285,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55766,SRR10753237,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN712-S503=Aug1_Cell_75.fastq.gz run1696_lane2_read2_indexN712-S503=Aug1_Cell_75.fastq.gz,fastq fastq,349436850.0,2329579.0,GSM4230287 r27,0:75 1:75,A:97251265;C:76806628;G:77656677;T:97675062;N:47218,75,75,,,97251265,76806628,77656677,97675062,47218,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90399,0.90953,0.22592,0.22897,0.90962,0.91015,0.48568,0.48353,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55767,SRR10753238,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S504=Aug1_Cell_76.fastq.gz run1696_lane2_read2_indexN701-S504=Aug1_Cell_76.fastq.gz,fastq fastq,287349300.0,1915662.0,GSM4230287 r28,0:75 1:75,A:79830728;C:63683589;G:64040532;T:79755658;N:38793,75,75,,,79830728,63683589,64040532,79755658,38793,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91249,0.91836,0.18353,0.18679,0.91942,0.91918,0.48879,0.48925,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55768,SRR10753239,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S505=Aug1_Cell_77.fastq.gz run1696_lane2_read2_indexN702-S505=Aug1_Cell_77.fastq.gz,fastq fastq,288709800.0,1924732.0,GSM4230287 r29,0:75 1:75,A:79556851;C:64127745;G:64891546;T:80093515;N:40143,75,75,,,79556851,64127745,64891546,80093515,40143,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90821,0.91323,0.185,0.18708,0.89018,0.89057,0.48437,0.48334,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55769,SRR10753240,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN709-S503=Aug1_Cell_51.fastq.gz run1696_lane2_read2_indexN709-S503=Aug1_Cell_51.fastq.gz,fastq fastq,241206600.0,1608044.0,GSM4230287 r3,0:75 1:75,A:66846250;C:53388095;G:53773714;T:67165505;N:33036,75,75,,,66846250,53388095,53773714,67165505,33036,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90761,0.91183,0.20482,0.2069,0.91437,0.91435,0.50196,0.50907,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55770,SRR10753241,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S506=Aug1_Cell_78.fastq.gz run1696_lane2_read2_indexN703-S506=Aug1_Cell_78.fastq.gz,fastq fastq,350680950.0,2337873.0,GSM4230287 r30,0:75 1:75,A:97180433;C:77760723;G:78449256;T:97242648;N:47890,75,75,,,97180433,77760723,78449256,97242648,47890,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91178,0.9175,0.18486,0.1874,0.91463,0.91612,0.51946,0.52606,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55771,SRR10753242,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN704-S507=Aug1_Cell_79.fastq.gz run1696_lane2_read2_indexN704-S507=Aug1_Cell_79.fastq.gz,fastq fastq,301610700.0,2010738.0,GSM4230287 r31,0:75 1:75,A:83008152;C:67488146;G:68027086;T:83048256;N:39060,75,75,,,83008152,67488146,68027086,83048256,39060,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90738,0.92127,0.1374,0.14115,0.90281,0.90323,0.49906,0.5053,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55772,SRR10753243,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN705-S508=Aug1_Cell_80.fastq.gz run1696_lane2_read2_indexN705-S508=Aug1_Cell_80.fastq.gz,fastq fastq,376354800.0,2509032.0,GSM4230287 r32,0:75 1:75,A:103364840;C:83901867;G:84865220;T:104170582;N:52291,75,75,,,103364840,83901867,84865220,104170582,52291,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.9055,0.91077,0.15298,0.1558,0.89116,0.89167,0.48355,0.48618,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55773,SRR10753244,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN711-S517=Aug1_Cell_81.fastq.gz run1696_lane2_read2_indexN711-S517=Aug1_Cell_81.fastq.gz,fastq fastq,299770350.0,1998469.0,GSM4230287 r33,0:75 1:75,A:82289754;C:67187388;G:67586885;T:82664262;N:42061,75,75,,,82289754,67187388,67586885,82664262,42061,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91515,0.92029,0.16415,0.16637,0.93576,0.9357,0.45125,0.44424,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55774,SRR10753245,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN712-S502=Aug1_Cell_82.fastq.gz run1696_lane2_read2_indexN712-S502=Aug1_Cell_82.fastq.gz,fastq fastq,324078300.0,2160522.0,GSM4230287 r34,0:75 1:75,A:88656173;C:73899158;G:74013418;T:87465839;N:43712,75,75,,,88656173,73899158,74013418,87465839,43712,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91408,0.91846,0.24394,0.246,0.96112,0.961,0.4816,0.59275,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55775,SRR10753246,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S503=Aug1_Cell_83.fastq.gz run1696_lane2_read2_indexN701-S503=Aug1_Cell_83.fastq.gz,fastq fastq,217032750.0,1446885.0,GSM4230287 r35,0:75 1:75,A:59534071;C:48070176;G:49062629;T:60336044;N:29830,75,75,,,59534071,48070176,49062629,60336044,29830,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.87055,0.87748,0.24417,0.24556,0.93943,0.93935,0.7874,0.78699,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55776,SRR10753247,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S504=Aug1_Cell_84.fastq.gz run1696_lane2_read2_indexN702-S504=Aug1_Cell_84.fastq.gz,fastq fastq,288801450.0,1925343.0,GSM4230287 r36,0:75 1:75,A:80110712;C:64112359;G:64456856;T:80083340;N:38183,75,75,,,80110712,64112359,64456856,80083340,38183,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91114,0.91718,0.16956,0.17377,0.91411,0.91429,0.50676,0.50753,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55777,SRR10753248,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S505=Aug1_Cell_85.fastq.gz run1696_lane2_read2_indexN703-S505=Aug1_Cell_85.fastq.gz,fastq fastq,296308500.0,1975390.0,GSM4230287 r37,0:75 1:75,A:82776201;C:64434147;G:65242392;T:83815687;N:40073,75,75,,,82776201,64434147,65242392,83815687,40073,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89013,0.89653,0.18828,0.19101,0.88787,0.88785,0.49705,0.505,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55778,SRR10753249,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN704-S506=Aug1_Cell_86.fastq.gz run1696_lane2_read2_indexN704-S506=Aug1_Cell_86.fastq.gz,fastq fastq,329897850.0,2199319.0,GSM4230287 r38,0:75 1:75,A:91441750;C:72960353;G:73464989;T:91986497;N:44261,75,75,,,91441750,72960353,73464989,91986497,44261,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91815,0.92369,0.18544,0.18829,0.94527,0.94552,0.4292,0.43583,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55779,SRR10753250,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN705-S507=Aug1_Cell_87.fastq.gz run1696_lane2_read2_indexN705-S507=Aug1_Cell_87.fastq.gz,fastq fastq,322963500.0,2153090.0,GSM4230287 r39,0:75 1:75,A:88789292;C:72352695;G:72843334;T:88935120;N:43059,75,75,,,88789292,72352695,72843334,88935120,43059,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.92095,0.92789,0.14339,0.14586,0.94308,0.94359,0.49931,0.4992,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55780,SRR10753251,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN710-S504=Aug1_Cell_52.fastq.gz run1696_lane2_read2_indexN710-S504=Aug1_Cell_52.fastq.gz,fastq fastq,265346250.0,1768975.0,GSM4230287 r4,0:75 1:75,A:74074058;C:58293208;G:58627997;T:74316626;N:34361,75,75,,,74074058,58293208,58627997,74316626,34361,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90624,0.9193,0.21417,0.22055,0.90948,0.90938,0.49135,0.48435,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55781,SRR10753252,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN706-S508=Aug1_Cell_88.fastq.gz run1696_lane2_read2_indexN706-S508=Aug1_Cell_88.fastq.gz,fastq fastq,346084350.0,2307229.0,GSM4230287 r40,0:75 1:75,A:95282196;C:77387933;G:77889452;T:95477032;N:47737,75,75,,,95282196,77387933,77889452,95477032,47737,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91441,0.91887,0.14069,0.14283,0.91589,0.91589,0.48567,0.48486,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55782,SRR10753253,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN712-S517=Aug1_Cell_89.fastq.gz run1696_lane2_read2_indexN712-S517=Aug1_Cell_89.fastq.gz,fastq fastq,299214150.0,1994761.0,GSM4230287 r41,0:75 1:75,A:84760328;C:64330889;G:64713377;T:85368909;N:40647,75,75,,,84760328,64330889,64713377,85368909,40647,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89925,0.9046,0.23324,0.23787,0.93754,0.93787,0.49809,0.49658,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55783,SRR10753254,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S502=Aug1_Cell_90.fastq.gz run1696_lane2_read2_indexN701-S502=Aug1_Cell_90.fastq.gz,fastq fastq,296379750.0,1975865.0,GSM4230287 r42,0:75 1:75,A:84724008;C:64477005;G:63594204;T:83543595;N:40938,75,75,,,84724008,64477005,63594204,83543595,40938,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91759,0.92318,0.59672,0.60102,0.9489,0.94884,0.51902,0.51562,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55784,SRR10753255,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S503=Aug1_Cell_91.fastq.gz run1696_lane2_read2_indexN702-S503=Aug1_Cell_91.fastq.gz,fastq fastq,381532350.0,2543549.0,GSM4230287 r43,0:75 1:75,A:104927348;C:85478286;G:86116958;T:104958903;N:50855,75,75,,,104927348,85478286,86116958,104958903,50855,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90434,0.90948,0.21281,0.2161,0.90609,0.90652,0.48698,0.48654,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55785,SRR10753256,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S504=Aug1_Cell_92.fastq.gz run1696_lane2_read2_indexN703-S504=Aug1_Cell_92.fastq.gz,fastq fastq,277685850.0,1851239.0,GSM4230287 r44,0:75 1:75,A:77163713;C:61411043;G:61889515;T:77184100;N:37479,75,75,,,77163713,61411043,61889515,77184100,37479,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89942,0.90575,0.19557,0.19955,0.92514,0.92659,0.50956,0.51364,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55786,SRR10753257,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN704-S505=Aug1_Cell_93.fastq.gz run1696_lane2_read2_indexN704-S505=Aug1_Cell_93.fastq.gz,fastq fastq,287073450.0,1913823.0,GSM4230287 r45,0:75 1:75,A:80239990;C:62929136;G:63425774;T:80441246;N:37304,75,75,,,80239990,62929136,63425774,80441246,37304,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90019,0.91389,0.16561,0.16949,0.90946,0.9092,0.44449,0.49777,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55787,SRR10753258,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN705-S506=Aug1_Cell_94.fastq.gz run1696_lane2_read2_indexN705-S506=Aug1_Cell_94.fastq.gz,fastq fastq,285636450.0,1904243.0,GSM4230287 r46,0:75 1:75,A:80380364;C:61727196;G:62532553;T:80957412;N:38925,75,75,,,80380364,61727196,62532553,80957412,38925,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.88701,0.89489,0.28158,0.28356,0.9391,0.94026,0.62885,0.62711,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55788,SRR10753259,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN706-S507=Aug1_Cell_95.fastq.gz run1696_lane2_read2_indexN706-S507=Aug1_Cell_95.fastq.gz,fastq fastq,319043700.0,2126958.0,GSM4230287 r47,0:75 1:75,A:88834179;C:69902391;G:70666753;T:89598537;N:41840,75,75,,,88834179,69902391,70666753,89598537,41840,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90283,0.90836,0.21154,0.21543,0.91082,0.91143,0.49488,0.48046,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55789,SRR10753260,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN707-S508=Aug1_Cell_96.fastq.gz run1696_lane2_read2_indexN707-S508=Aug1_Cell_96.fastq.gz,fastq fastq,23619300.0,157462.0,GSM4230287 r48,0:75 1:75,A:6648282;C:5444230;G:4975645;T:6548172;N:2971,75,75,,,6648282,5444230,4975645,6548172,2971,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.72054,0.86233,0.11482,0.14219,0.95556,0.95627,0.46808,0.46497,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55790,SRR10753261,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN711-S505=Aug1_Cell_53.fastq.gz run1696_lane2_read2_indexN711-S505=Aug1_Cell_53.fastq.gz,fastq fastq,306382800.0,2042552.0,GSM4230287 r5,0:75 1:75,A:86067136;C:66550597;G:67047629;T:86675235;N:42203,75,75,,,86067136,66550597,67047629,86675235,42203,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90104,0.90602,0.25949,0.26321,0.94073,0.94091,0.51681,0.46212,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55791,SRR10753262,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN712-S506=Aug1_Cell_54.fastq.gz run1696_lane2_read2_indexN712-S506=Aug1_Cell_54.fastq.gz,fastq fastq,351081900.0,2340546.0,GSM4230287 r6,0:75 1:75,A:98081793;C:77038508;G:77373196;T:98539502;N:48901,75,75,,,98081793,77038508,77373196,98539502,48901,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90946,0.91275,0.18599,0.18944,0.91995,0.92064,0.51022,0.51557,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55792,SRR10753263,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN701-S507=Aug1_Cell_55.fastq.gz run1696_lane2_read2_indexN701-S507=Aug1_Cell_55.fastq.gz,fastq fastq,313116300.0,2087442.0,GSM4230287 r7,0:75 1:75,A:88330056;C:67596816;G:68042817;T:89103852;N:42759,75,75,,,88330056,67596816,68042817,89103852,42759,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89433,0.89911,0.27071,0.27406,0.90234,0.9025,0.49714,0.49217,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55793,SRR10753264,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S508=Aug1_Cell_56.fastq.gz run1696_lane2_read2_indexN702-S508=Aug1_Cell_56.fastq.gz,fastq fastq,337006050.0,2246707.0,GSM4230287 r8,0:75 1:75,A:91946919;C:76067774;G:76661595;T:92284491;N:45271,75,75,,,91946919,76067774,76661595,92284491,45271,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.921,0.92486,0.10214,0.10415,0.89528,0.89591,0.4974,0.48846,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55794,SRR10753265,SRX7427899,SRS5873832,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Aug1 2016 20ss etv2gfp,GSM4230287,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,Aug1 2016 20ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:20 somite stage,GSM4230287,GSM4230287: Aug1 2016 20ss etv2gfp; Danio rerio; RNA Seq,GSM4230287,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230287,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN708-S517=Aug1_Cell_57.fastq.gz run1696_lane2_read2_indexN708-S517=Aug1_Cell_57.fastq.gz,fastq fastq,264639450.0,1764263.0,GSM4230287 r9,0:75 1:75,A:74195564;C:57388120;G:58187904;T:74832787;N:35075,75,75,,,74195564,57388120,58187904,74832787,35075,SRX7427899,SRS5873832,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89601,0.9097,0.3037,0.31018,0.92133,0.92028,0.52888,0.54457,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55795,SRR10753170,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read2_indexN701-S517=Jul11_Cell_1.fastq.gz run1696_lane2_read1_indexN701-S517=Jul11_Cell_1.fastq.gz,fastq fastq,234610050.0,1564067.0,GSM4230286 r1,0:75 1:75,A:65886611;C:50927760;G:51256089;T:66507455;N:32135,75,75,,,65886611,50927760,51256089,66507455,32135,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90542,0.91089,0.2189,0.22149,0.88373,0.88394,0.4997,0.50524,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55796,SRR10753171,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S502=Jul11_Cell_10.fastq.gz run1696_lane2_read2_indexN703-S502=Jul11_Cell_10.fastq.gz,fastq fastq,229833900.0,1532226.0,GSM4230286 r10,0:75 1:75,A:64620859;C:49968774;G:50168025;T:65045353;N:30889,75,75,,,64620859,49968774,50168025,65045353,30889,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90987,0.91683,0.23924,0.24284,0.93663,0.9373,0.51987,0.51778,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55797,SRR10753172,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN704-S503=Jul11_Cell_11.fastq.gz run1696_lane2_read2_indexN704-S503=Jul11_Cell_11.fastq.gz,fastq fastq,263149800.0,1754332.0,GSM4230286 r11,0:75 1:75,A:73836706;C:57360247;G:57722644;T:74193453;N:36750,75,75,,,73836706,57360247,57722644,74193453,36750,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89945,0.90639,0.23998,0.24336,0.91133,0.91086,0.51231,0.51605,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55798,SRR10753173,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN705-S504=Jul11_Cell_12.fastq.gz run1696_lane2_read2_indexN705-S504=Jul11_Cell_12.fastq.gz,fastq fastq,244566900.0,1630446.0,GSM4230286 r12,0:75 1:75,A:68319904;C:53659268;G:53938996;T:68614934;N:33798,75,75,,,68319904,53659268,53938996,68614934,33798,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91004,0.9178,0.25315,0.25664,0.92249,0.92326,0.48563,0.48143,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55799,SRR10753174,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN706-S505=Jul11_Cell_13.fastq.gz run1696_lane2_read2_indexN706-S505=Jul11_Cell_13.fastq.gz,fastq fastq,241816350.0,1612109.0,GSM4230286 r13,0:75 1:75,A:67268594;C:53259507;G:53453143;T:67801071;N:34035,75,75,,,67268594,53259507,53453143,67801071,34035,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90542,0.91154,0.1938,0.19642,0.92486,0.92569,0.5072,0.50859,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55800,SRR10753175,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN707-S506=Jul11_Cell_14.fastq.gz run1696_lane2_read2_indexN707-S506=Jul11_Cell_14.fastq.gz,fastq fastq,310674300.0,2071162.0,GSM4230286 r14,0:75 1:75,A:85680219;C:69325072;G:69483001;T:86144244;N:41764,75,75,,,85680219,69325072,69483001,86144244,41764,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90512,0.91232,0.18685,0.18956,0.92234,0.92218,0.51203,0.50944,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55801,SRR10753176,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN708-S507=Jul11_Cell_15.fastq.gz run1696_lane2_read2_indexN708-S507=Jul11_Cell_15.fastq.gz,fastq fastq,245494500.0,1636630.0,GSM4230286 r15,0:75 1:75,A:68708098;C:53710501;G:54106787;T:68935732;N:33382,75,75,,,68708098,53710501,54106787,68935732,33382,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90285,0.90822,0.20608,0.20968,0.91658,0.91679,0.48453,0.48898,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55802,SRR10753177,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN709-S508=Jul11_Cell_16.fastq.gz run1696_lane2_read2_indexN709-S508=Jul11_Cell_16.fastq.gz,fastq fastq,271221000.0,1808140.0,GSM4230286 r16,0:75 1:75,A:75487866;C:59716126;G:59980018;T:76001099;N:35891,75,75,,,75487866,59716126,59980018,76001099,35891,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91439,0.91827,0.22378,0.22488,0.91094,0.91098,0.45947,0.46059,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55803,SRR10753178,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S517=Jul11_Cell_17.fastq.gz run1696_lane2_read2_indexN703-S517=Jul11_Cell_17.fastq.gz,fastq fastq,245749650.0,1638331.0,GSM4230286 r17,0:75 1:75,A:69131081;C:53395543;G:53713791;T:69474613;N:34622,75,75,,,69131081,53395543,53713791,69474613,34622,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89587,0.91024,0.25975,0.26614,0.92776,0.92813,0.51292,0.50379,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55804,SRR10753179,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN704-S502=Jul11_Cell_18.fastq.gz run1696_lane2_read2_indexN704-S502=Jul11_Cell_18.fastq.gz,fastq fastq,278149650.0,1854331.0,GSM4230286 r18,0:75 1:75,A:76409981;C:62370498;G:62741308;T:76589811;N:38052,75,75,,,76409981,62370498,62741308,76589811,38052,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91432,0.92011,0.0909,0.09223,0.91516,0.91504,0.50915,0.51367,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55805,SRR10753180,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN705-S503=Jul11_Cell_19.fastq.gz run1696_lane2_read2_indexN705-S503=Jul11_Cell_19.fastq.gz,fastq fastq,290396700.0,1935978.0,GSM4230286 r19,0:75 1:75,A:79088001;C:65776138;G:66234495;T:79259307;N:38759,75,75,,,79088001,65776138,66234495,79259307,38759,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.9257,0.93018,0.15935,0.16195,0.91559,0.91561,0.47189,0.47975,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55806,SRR10753181,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN702-S502=Jul11_Cell_2.fastq.gz run1696_lane2_read2_indexN702-S502=Jul11_Cell_2.fastq.gz,fastq fastq,199779150.0,1331861.0,GSM4230286 r2,0:75 1:75,A:55573073;C:44137788;G:44371358;T:55669229;N:27702,75,75,,,55573073,44137788,44371358,55669229,27702,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.9054,0.91064,0.17571,0.17809,0.91979,0.91979,0.51339,0.51495,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55807,SRR10753182,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN706-S504=Jul11_Cell_20.fastq.gz run1696_lane2_read2_indexN706-S504=Jul11_Cell_20.fastq.gz,fastq fastq,98432550.0,656217.0,GSM4230286 r20,0:75 1:75,A:28957084;C:19849684;G:19985734;T:29626805;N:13243,75,75,,,28957084,19849684,19985734,29626805,13243,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.84163,0.8548,0.45261,0.46012,0.96175,0.96244,0.89566,0.88797,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55808,SRR10753183,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN707-S505=Jul11_Cell_21.fastq.gz run1696_lane2_read2_indexN707-S505=Jul11_Cell_21.fastq.gz,fastq fastq,240352350.0,1602349.0,GSM4230286 r21,0:75 1:75,A:68296941;C:52691153;G:52436339;T:66894877;N:33040,75,75,,,68296941,52691153,52436339,66894877,33040,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91789,0.92502,0.53906,0.54283,0.94949,0.95055,0.52294,0.521,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55809,SRR10753184,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN708-S506=Jul11_Cell_22.fastq.gz run1696_lane2_read2_indexN708-S506=Jul11_Cell_22.fastq.gz,fastq fastq,246827700.0,1645518.0,GSM4230286 r22,0:75 1:75,A:67537552;C:55581780;G:55806146;T:67868782;N:33440,75,75,,,67537552,55581780,55806146,67868782,33440,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91202,0.92695,0.10399,0.10676,0.9304,0.93042,0.49498,0.50126,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55810,SRR10753185,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN709-S507=Jul11_Cell_23.fastq.gz run1696_lane2_read2_indexN709-S507=Jul11_Cell_23.fastq.gz,fastq fastq,169590450.0,1130603.0,GSM4230286 r23,0:75 1:75,A:47628900;C:36822280;G:36950916;T:48165962;N:22392,75,75,,,47628900,36822280,36950916,48165962,22392,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89164,0.89851,0.34871,0.35219,0.93407,0.9349,0.50768,0.49949,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55811,SRR10753186,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN710-S508=Jul11_Cell_24.fastq.gz run1696_lane2_read2_indexN710-S508=Jul11_Cell_24.fastq.gz,fastq fastq,305726550.0,2038177.0,GSM4230286 r24,0:75 1:75,A:81533250;C:71041934;G:71418199;T:81693555;N:39612,75,75,,,81533250,71041934,71418199,81693555,39612,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.93226,0.93694,0.10993,0.11159,0.89729,0.89759,0.45219,0.45531,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55812,SRR10753187,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN704-S517=Jul11_Cell_25.fastq.gz run1696_lane2_read2_indexN704-S517=Jul11_Cell_25.fastq.gz,fastq fastq,286256850.0,1908379.0,GSM4230286 r25,0:75 1:75,A:80047739;C:62886333;G:63017723;T:80266939;N:38116,75,75,,,80047739,62886333,63017723,80266939,38116,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90362,0.90979,0.24338,0.24655,0.93316,0.93251,0.49351,0.49478,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55813,SRR10753188,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN705-S502=Jul11_Cell_26.fastq.gz run1696_lane2_read2_indexN705-S502=Jul11_Cell_26.fastq.gz,fastq fastq,306193950.0,2041293.0,GSM4230286 r26,0:75 1:75,A:86358269;C:66156274;G:66649467;T:86988153;N:41787,75,75,,,86358269,66156274,66649467,86988153,41787,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90067,0.90677,0.25859,0.26196,0.90193,0.90177,0.48253,0.48139,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55814,SRR10753189,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN706-S503=Jul11_Cell_27.fastq.gz run1696_lane2_read2_indexN706-S503=Jul11_Cell_27.fastq.gz,fastq fastq,313345650.0,2088971.0,GSM4230286 r27,0:75 1:75,A:82621143;C:73782332;G:74207186;T:82692158;N:42831,75,75,,,82621143,73782332,74207186,82692158,42831,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.92039,0.92528,0.04806,0.04957,0.96262,0.96313,0.50982,0.51915,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55815,SRR10753190,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN707-S504=Jul11_Cell_28.fastq.gz run1696_lane2_read2_indexN707-S504=Jul11_Cell_28.fastq.gz,fastq fastq,290251800.0,1935012.0,GSM4230286 r28,0:75 1:75,A:81001873;C:63853844;G:64184343;T:81173703;N:38037,75,75,,,81001873,63853844,64184343,81173703,38037,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90735,0.91191,0.22917,0.23283,0.89822,0.89913,0.50645,0.50208,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55816,SRR10753191,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN708-S505=Jul11_Cell_29.fastq.gz run1696_lane2_read2_indexN708-S505=Jul11_Cell_29.fastq.gz,fastq fastq,269796600.0,1798644.0,GSM4230286 r29,0:75 1:75,A:74845520;C:59720345;G:60026981;T:75166629;N:37125,75,75,,,74845520,59720345,60026981,75166629,37125,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.8986,0.9055,0.25151,0.25413,0.92622,0.92592,0.51342,0.5192,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55817,SRR10753192,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN703-S503=Jul11_Cell_3.fastq.gz run1696_lane2_read2_indexN703-S503=Jul11_Cell_3.fastq.gz,fastq fastq,276661350.0,1844409.0,GSM4230286 r3,0:75 1:75,A:76019778;C:61876096;G:62360417;T:76368352;N:36707,75,75,,,76019778,61876096,62360417,76368352,36707,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91319,0.91876,0.16398,0.16607,0.90429,0.90506,0.48848,0.48811,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55818,SRR10753193,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN709-S506=Jul11_Cell_30.fastq.gz run1696_lane2_read2_indexN709-S506=Jul11_Cell_30.fastq.gz,fastq fastq,261668550.0,1744457.0,GSM4230286 r30,0:75 1:75,A:71791262;C:58938302;G:59235753;T:71668176;N:35057,75,75,,,71791262,58938302,59235753,71668176,35057,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91876,0.9245,0.1575,0.15921,0.92851,0.9292,0.47013,0.46545,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55819,SRR10753194,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN710-S507=Jul11_Cell_31.fastq.gz run1696_lane2_read2_indexN710-S507=Jul11_Cell_31.fastq.gz,fastq fastq,255239700.0,1701598.0,GSM4230286 r31,0:75 1:75,A:67813778;C:59696558;G:59917854;T:67778135;N:33375,75,75,,,67813778,59696558,59917854,67778135,33375,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89552,0.91108,0.04489,0.04637,0.95112,0.9515,0.45372,0.45598,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55820,SRR10753195,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN711-S508=Jul11_Cell_32.fastq.gz run1696_lane2_read2_indexN711-S508=Jul11_Cell_32.fastq.gz,fastq fastq,279591150.0,1863941.0,GSM4230286 r32,0:75 1:75,A:77184098;C:62287058;G:62715923;T:77365240;N:38831,75,75,,,77184098,62287058,62715923,77365240,38831,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90124,0.90862,0.17316,0.17598,0.92186,0.922,0.47028,0.46696,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55821,SRR10753196,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN705-S517=Jul11_Cell_33.fastq.gz run1696_lane2_read2_indexN705-S517=Jul11_Cell_33.fastq.gz,fastq fastq,297679350.0,1984529.0,GSM4230286 r33,0:75 1:75,A:81908338;C:66248702;G:67048123;T:82433762;N:40425,75,75,,,81908338,66248702,67048123,82433762,40425,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.90869,0.91575,0.229,0.23301,0.92277,0.9233,0.50453,0.50635,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55822,SRR10753197,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN706-S502=Jul11_Cell_34.fastq.gz run1696_lane2_read2_indexN706-S502=Jul11_Cell_34.fastq.gz,fastq fastq,272841900.0,1818946.0,GSM4230286 r34,0:75 1:75,A:77037069;C:58741674;G:59336039;T:77689813;N:37305,75,75,,,77037069,58741674,59336039,77689813,37305,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.89543,0.90089,0.26126,0.26467,0.9301,0.93038,0.50919,0.5099,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55823,SRR10753198,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN707-S503=Jul11_Cell_35.fastq.gz run1696_lane2_read2_indexN707-S503=Jul11_Cell_35.fastq.gz,fastq fastq,310282350.0,2068549.0,GSM4230286 r35,0:75 1:75,A:85765859;C:68996693;G:69277107;T:86202149;N:40542,75,75,,,85765859,68996693,69277107,86202149,40542,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91045,0.91657,0.1709,0.17439,0.94387,0.94351,0.47308,0.45,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55824,SRR10753199,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN708-S504=Jul11_Cell_36.fastq.gz run1696_lane2_read2_indexN708-S504=Jul11_Cell_36.fastq.gz,fastq fastq,283378950.0,1889193.0,GSM4230286 r36,0:75 1:75,A:78951358;C:62596074;G:62824427;T:78970041;N:37050,75,75,,,78951358,62596074,62824427,78970041,37050,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.91007,0.91766,0.21216,0.21655,0.9037,0.90392,0.48958,0.4883,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System
55825,SRR10753200,SRX7427898,SRS5873831,SRP238479,PRJNA597148,Single cell transcriptomic analysis of embryonic vasculogenesis identifies the conversion of Etv2 deficient vascular progenitors into skeletal muscle,GSE142484,Transcriptome Analysis,During vertebrate embryogenesis  vascular endothelial cells originate in the lateral plate mesoderm LPM next to the progenitors of skeletal muscle. It is currently not clear what prevents vascular progenitors from responding to the adjacent signals that promote muscle development. An ETS transcription factor Etv2 functions as an evolutionarily conserved master regulator of vasculogenesis. Here we performed single cell transcriptomic analysis of hematovascular development in wild type and etv2 mutant zebrafish embryos. Distinct transcriptional signatures of different types of hematopoietic and vascular progenitors were identified using an etv2ci32Gt gene trap line  in which Gal4 transcriptional activator has integrated into the etv2 gene locus. Unexpectedly  a cell population with the skeletal muscle signature was observed in etv2 deficient embryos. We demonstrate that multiple etv2ci32Gt; UAS:GFP cells migrate into the somites  elongate and differentiate as skeletal muscle cells instead of contributing to vasculature in etv2 deficient embryos. Wnt and FGF signaling promoted the differentiation of these putative multipotent etv2 progenitor cells into skeletal muscle cells. We conclude that etv2 actively represses muscle differentiation in vascular progenitors  thus locking these cells into vascular endothelial fate. We also identified the transcriptional signature of putative multipotent progenitors within the LPM that may give rise to vascular progenitor and skeletal muscle cells. Finally  we demonstrate that arterial progenitors co express multiple arterial and venous markers during early stages of vasculogenesis  suggesting multi potency of early vascular progenitors.These findings will be important in understanding the ontogeny of different mesodermal lineages and will help in designing in vitro differentiation strategies to generate vascular  muscle and other types of progenitors for therapeutic purposes. Overall design: 96 cells 48 cells each,,pubmed:32493965,,Jul11 2016 15 18ss etv2gfp,GSM4230286,,tissue:Vascular Endothelial Cells|cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,Jul11 2016 15 18ss etv2gfp,Alignment with Kallisto/AltAnalyze Iterative clustering and guide gene selection ICGS with cosine similarity and fold cutoff of 6 with a minimum of 5 cells and conservative filtering for cell cycle effects Markerfinder to identify enriched genes in each group Genome build: Zv9 Ensembl release 72,Vascular Endothelial Cells,No treatment,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,Embryos grown in standard E3 medium at 28.5C,cell type:Vascular Endothelial Cells|animal line:Tg 2.3 etv2:GFPzf372|developmental stage:15 18 somite stage,GSM4230286,GSM4230286: Jul11 2016 15 18ss etv2gfp; Danio rerio; RNA Seq,GSM4230286,,1,Embryos were non enzymatically homogenized and filtered to create single cells suspension followed by FACs to isolate GFP+ cells,GEO Accession:GSM4230286,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP238479,,,run1696_lane2_read1_indexN709-S505=Jul11_Cell_37.fastq.gz run1696_lane2_read2_indexN709-S505=Jul11_Cell_37.fastq.gz,fastq fastq,179160000.0,1194400.0,GSM4230286 r37,0:75 1:75,A:51136454;C:37981592;G:38236085;T:51782634;N:23235,75,75,,,51136454,37981592,38236085,51782634,23235,SRX7427898,SRS5873831,SRA1015481,GEO,"Developmental Biology, Cincinnati Children's Hospital Medical Center",2,0.8769,0.885,0.44874,0.4538,0.94945,0.95004,0.62021,0.62468,75,75,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2019-12-21,Segmentation,Embryo,Endothelium,Cardiovascular System