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76 rows where devstage_curation = "Segmentation" and technology = "smartseq"

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experiment.library_strategy 2

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technology 1

  • smartseq · 76 ✖

experiment.platform 1

experiment.library_source 1

devstage_curation_coarse 1

devstage_curation 1

  • Segmentation · 76 ✖
Link rowid ▼ run.accession experiment.accession sample.accession study.accession bioproject study.title study.alias study.type study.abstract study.attributes study.PMIDs sample.description sample.title sample.alias sample.centername sample.attributes GEOsample.title GEOsample.dataprocessing GEOsample.source GEOsample.treatmentprotocol GEOsample.extractprotocol GEOsample.growthprotocol GEOsample.characteristics GEOsample.accession experiment.title experiment.alias experiment.library_name experiment.design_description experiment.library_construction_protocol experiment.attributes experiment.library_strategy experiment.library_source experiment.library_selection experiment.library_layout experiment.platform experiment.instrument_model experiment.spot_descriptor experiment.study_ref run.title run.attributes run.filename run.semantic_name run.total_bases run.total_spots run.alias run.read_lengths run.base_counts run.r1_length run.r2_length run.r3_length run.r4_length run.Acount run.Ccount run.Gcount run.Tcount run.Ncount run.experiment run.pool_member submission.accession submission.srasource submission.bioprojectsource seqdetective.n_mates seqdetective.mapping_rate.mate1 seqdetective.mapping_rate.mate2 seqdetective.nofeature_rate.mate1 seqdetective.nofeature_rate.mate2 seqdetective.sparsity.mate1 seqdetective.sparsity.mate2 seqdetective.pos_strand_rate.mate1 seqdetective.pos_strand_rate.mate2 seqdetective.readlen.mate1 seqdetective.readlen.mate2 seqdetective.judgement.mate1 seqdetective.judgement.mate2 seqdetective.judgement.reason platform_family instrument_generation read_bias selection_class prep_kit sc_or_bulk tech_class technology tech_variant submission.bioprojectsource.country earliest_date devstage_curation devstage_curation_coarse tissue_curation tissue_curation_coarse
9787 9787 ERR3838742 ERX3851408 ERS4266432 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma 10somites rep2 SAMEA6501983 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501983|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 10somites rep2|age:14|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 10somites rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma 10somites rep2 p Soma 10somites rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S6_R1.fastq.gz S6_R2.fastq.gz fastq fastq 1244080980.0 8338002.0 E MTAB 8707:S6 R 0:74.60 1:74.60 A:356418931;C:263292901;G:270630630;T:353140798;N:597720 74 74     356418931 263292901 270630630 353140798 597720 ERX3851408 ERS4266432 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.86791 0.86732 0.20223 0.20398 0.75588 0.75883 0.4862 0.48313 76 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Segmentation Embryo Whole Organism All anatomical structures
9788 9788 ERR3838741 ERX3851407 ERS4266431 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Soma 10somites rep1 SAMEA6501982 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501982|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:Soma 10somites rep1|age:14|broker name:ArrayExpress|cell type:whole embryo|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:Soma 10somites rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:Soma 10somites rep1 p Soma 10somites rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:whole embryo OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S4_R1.fastq.gz S4_R2.fastq.gz fastq fastq 946153328.0 6354843.0 E MTAB 8707:S4 R 0:74.44 1:74.45 A:268310887;C:203457903;G:208969410;T:264875129;N:539999 74 74     268310887 203457903 208969410 264875129 539999 ERX3851407 ERS4266431 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.92415 0.92372 0.12138 0.12268 0.74061 0.74422 0.47246 0.47448 76 76 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Segmentation Embryo Whole Organism All anatomical structures
9801 9801 ERR3838728 ERX3851394 ERS4266418 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC 10somites rep2 SAMEA6501969 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501969|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 10somites rep2|age:14|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 10somites rep2|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC 10somites rep2 p PGC 10somites rep2 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S5_R1.fastq.gz S5_R2.fastq.gz fastq fastq 1186993033.0 7958634.0 E MTAB 8707:S5 R 0:74.57 1:74.58 A:332263881;C:259239478;G:267014990;T:327946611;N:528073 74 74     332263881 259239478 267014990 327946611 528073 ERX3851394 ERS4266418 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.90713 0.9062 0.10071 0.1016 0.73058 0.73279 0.48458 0.48038 74 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Segmentation Embryo Whole Organism All anatomical structures
9802 9802 ERR3838727 ERX3851393 ERS4266417 ERP119601 PRJEB36411 RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E-MTAB-8707 Transcriptome Analysis Zebrafish Primordial Germ Cells PGCs were tracked in the TgBuc GFP line where the germ plasm protein Buc is fused to GFP. GFP positive cells were isolated via FACS and RNA seq was performed on polyadenylated transcripts for PGCs and somatic cells at 256 cell high dome 10 somites and prim 5 stages. Two hundred cells were used for each biological replicate. RNA seq was also performed on embryos in where Tdrd7 translation was inhibited via morpholino treatment. ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24   Protocols: Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. PGC 10somites rep1 SAMEA6501968 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK ENA FIRST PUBLIC:2020 04 30T04:03:48Z|ENA LAST UPDATE:2020 01 24T08:44:00Z|External Id:SAMEA6501968|INSDC center name:MRC London Institute of Medical Sciences and Faculty of Medicine Imperial College London UK|INSDC first public:2020 04 30T04:03:48Z|INSDC last update:2020 01 24T08:44:00Z|INSDC status:public|Submitter Id:E MTAB 8707:PGC 10somites rep1|age:14|broker name:ArrayExpress|cell type:primordial germ cell|common name:zebrafish|developmental stage:10 somites|genotype:tgbuc:egfp|phenotype:fluorescent PGCs due to germ plasm localised GFP|sample name:E MTAB 8707:PGC 10somites rep1|scientific name:Danio rerio|strain:AB                 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis E MTAB 8707:PGC 10somites rep1 p PGC 10somites rep1 p RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis Zebrafish PGCs were isolated via FACS post embryo dissociation. The embryos were grown until the desired stage at 28.5C and collected in synchronous batches. Cell dissociation occurred via pipetting thoroughly up and down the pooled embryos until the solution appeared homogeneous. Yolk excess was removed by two rounds of centrifugation at 300 x g 5 minutes. Cells were passed through a 50 μm mesh and loaded into a FACS Aria II machine for cell sorting. Cells were lysed in presence of RNAse inhibitor 0.2 U/μl and cDNA generated from the cell lysate. cDNA was generated with the Takara SMART Seq® v4 Ultra® Low Input RNA Kit as from manufacturer's instruction. In brief reverse transcription was carried out in presence of the SMART Seq CDS Primer II A and SMARTScribeTM Reverse Transcriptase Takara Bio Europe 634889 France. Library amplification occurred according to protocol recommendations and the amplified cDNA purified via the Agencourt AMPure XP beads kit Beckman Coulter A63880 USA. Experimental Factor: developmental stage:10 somites|Experimental Factor: compound:n1|Experimental Factor: cell type:primordial germ cell OTHER TRANSCRIPTOMIC RANDOM PCR PAIRED ILLUMINA NextSeq 550   ERP119601 NextSeq 550 paired end sequencing; RNA seq of zebrafish primordial germ cells and somatic cells during early embryogenesis ENA FIRST PUBLIC:2020 12 24|ENA LAST UPDATE:2020 01 24 S3_R1.fastq.gz S3_R2.fastq.gz fastq fastq 1230551446.0 8251644.0 E MTAB 8707:S3 R 0:74.56 1:74.57 A:345409587;C:267720436;G:275626594;T:341185818;N:609011 74 74     345409587 267720436 275626594 341185818 609011 ERX3851393 ERS4266417 ERA2354529 MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive MRC London Institute of Medical Sciences and Faculty of Medicine, Imperial College, London, UK|European Nucleotide Archive 2 0.90983 0.90985 0.1005 0.10037 0.72622 0.72825 0.49116 0.49135 76 75 B B biological fallback assumption illumina nextseq unknown random_priming unknown sc single_cell_plate smartseq   United Kingdom 2020-01-24 Segmentation Embryo Whole Organism All anatomical structures
34551 34551 SRR32104356 SRX27449954 SRS23876475 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Positive CNC 3 GSM8751787   source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing 17hpf Positive CNC 3 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples cardiac neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry + GSM8751787 GSM8751787: 17hpf Positive CNC 3; Danio rerio; RNA Seq GSM8751787 r1 GSM8751787 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_pos_17hpf_CNC_3_22028_combined_filtered.fastq.gz fastq 5836253400.0 58362534.0 GSM8751787 r1 0:100 A:1666874971;C:1250406201;G:1263794016;T:1655113176;N:65036 100       1666874971 1250406201 1263794016 1655113176 65036 SRX27449954 SRS23876475 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Multi-tissue Multi-system
34552 34552 SRR32104357 SRX27449953 SRS23876474 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Positive CNC 2 GSM8751786   source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing 17hpf Positive CNC 2 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples cardiac neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry + GSM8751786 GSM8751786: 17hpf Positive CNC 2; Danio rerio; RNA Seq GSM8751786 r1 GSM8751786 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_pos_17hpf_CNC_2_21338_combined_filtered.fastq.gz fastq 2444486550.0 48889731.0 GSM8751786 r1 0:50 A:706384494;C:515182895;G:525593789;T:697319091;N:6281 50       706384494 515182895 525593789 697319091 6281 SRX27449953 SRS23876474 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Multi-tissue Multi-system
34553 34553 SRR32104358 SRX27449952 SRS23876472 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Positive CNC 1 GSM8751785   source name:cardiac neural crest from midbrain hindbrain boundary to somite 6|tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry +|geo loc name:missing|collection date:missing 17hpf Positive CNC 1 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples cardiac neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:cardiac neural crest from midbrain hindbrain boundary to somite 6|cell type:migratory cardiac neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry + GSM8751785 GSM8751785: 17hpf Positive CNC 1; Danio rerio; RNA Seq GSM8751785 r1 GSM8751785 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_pos_17hpf_CNC_1_21309_combined_filtered.fastq.gz fastq 3136080950.0 62721619.0 GSM8751785 r1 0:50 A:867446661;C:707750289;G:716376649;T:844460193;N:47158 50       867446661 707750289 716376649 844460193 47158 SRX27449952 SRS23876472 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Multi-tissue Multi-system
34554 34554 SRR32104359 SRX27449951 SRS23876473 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Negative CNC 3 GSM8751784   source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry |geo loc name:missing|collection date:missing 17hpf Negative CNC 3 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples non neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry GSM8751784 GSM8751784: 17hpf Negative CNC 3; Danio rerio; RNA Seq GSM8751784 r1 GSM8751784 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_neg_17hpf_CNC_3_22029_combined_filtered.fastq.gz fastq 6549316700.0 65493167.0 GSM8751784 r1 0:100 A:1904137226;C:1372226751;G:1395882591;T:1876995541;N:74591 100       1904137226 1372226751 1395882591 1876995541 74591 SRX27449951 SRS23876473 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Brain Nervous System
34555 34555 SRR32104360 SRX27449950 SRS23876471 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Negative CNC 2 GSM8751783   source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry |geo loc name:missing|collection date:missing 17hpf Negative CNC 2 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples non neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry GSM8751783 GSM8751783: 17hpf Negative CNC 2; Danio rerio; RNA Seq GSM8751783 r1 GSM8751783 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_neg_17hpf_CNC_2_21339_combined_filtered.fastq.gz fastq 2595442300.0 51908846.0 GSM8751783 r1 0:50 A:735396784;C:561568693;G:572114011;T:726356371;N:6441 50       735396784 561568693 572114011 726356371 6441 SRX27449950 SRS23876471 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Brain Nervous System
34556 34556 SRR32104361 SRX27449949 SRS23876470 SRP559533 PRJNA1214751 Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration [bulk RNA seq] GSE287815 Transcriptome Analysis During vertebrate development the heart primarily arises from mesoderm with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here by integrating bulk and single cell RNAseq with ATAC seq we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factors egr1 sox9a tfap2a and ets1. Notably we show that cells expressing the canonical neural crest gene sox10 are essential for proper cardiac regeneration in adult zebrafish. Furthermore expression of all transcription factors from the migratory cardiac crest gene subcircuit are xxx post injury at the wound edge. Together our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination with key factors re activated during regeneration. Overall design: Migratory cardiac neural crest cells mcherry + and non neural crest cells from the same tissue mcherry were FAC sorted from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos. Migratory trunk neural crest cells GFP + were FAC sorted from 24hpf Tg 4.9sox10:eGFP embryos.       17hpf Negative CNC 1 GSM8751782   source name:non neural crest from midbrain hindbrain boundary to somite 6|tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry |geo loc name:missing|collection date:missing 17hpf Negative CNC 1 Reads were mapped zebrafish genome GRCz10 using Bowtie 2. Transcript counts were determined using featureCounts Subread. Differential gene expression was performed using DEseq. Assembly: GRCz10 Supplementary files format and content: tab delimited text file included for cardiac neural crest and non neural crest samples non neural crest from midbrain hindbrain boundary to somite 6   mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   tissue:non neural crest from midbrain hindbrain boundary to somite 6|cell type:non neural crest|transgenic line:Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP|age:16 somite stage 17hpf|fluorophore:mcherry GSM8751782 GSM8751782: 17hpf Negative CNC 1; Danio rerio; RNA Seq GSM8751782 r1 GSM8751782 1 mch+ CdNC cells and mch non neural crest cells from 16 somite stage Tg 4.9sox10:GAL4 UAS cre;UAS:NfsB mCherry;myl7:nucGFP embryos were dissected dissociated and FAC sorted. GFP+ cells were sorted from 24hpf Tg 4.9sox10:eGFP embryos were dissected dissociated and FAC sorted. Tissues were dissociated in Accumax and then sorted BD FACSAria™ Fusion Flow Cytometer. cDNA was prepared from each sample using the SMART Seq® v4 Ultra® Low Input RNA Kit. Standard Illumina protocols were used to construct each sequencing library and an Illumina HiSeq2500 sequencer at the Millard and Muriel Jacobs Genetics and Genomics Laboratory California Institute of Technology Pasadena CA for 50 million single ended reads.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP559533     Sox10_neg_17hpf_CNC_1_21310_combined_filtered.fastq.gz fastq 2554400850.0 51088017.0 GSM8751782 r1 0:50 A:739730182;C:537827580;G:551508245;T:725296198;N:38645 50       739730182 537827580 551508245 725296198 38645 SRX27449949 SRS23876470 SRA2058978 Martik Lab, Molecular and Cell Biology, University of California Berkeley Martik Lab, Molecular and Cell Biology, University of California Berkeley                       B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2025-01-23 Segmentation Embryo Brain Nervous System
55474 55474 SRR10434088 SRX7130061 SRS5639405 SRP229597 PRJNA589032 mRNA profile of zebrafish periderm at 4 somite stage GSE139808 Transcriptome Analysis In order to compare the transcriptome and tissue specific nucleosome free regions of zebrafish periderm cells at 4 somite stage we isolated the RNA from sorted GFP positive cells of Tgkrt4:GFP embryos and perform low input RNA seq. This study revealed periderm specific transcriptome at 4 somite stage. Moreover comparing with ATAC seq from the same tissue we confirmed the correlation between gene expression and nearby chromatin accessibility. Overall design: GFP positive embryos were harvested from three independent incross of Tgkrt4:GFP. Embryos were dissociated and sorted with FACS. For each batch 2000 GFP positive and 2000 GFP negative cells were collected and subjected to RNA seq. parent bioproject:PRJNA589023 pubmed:32031521   GFP negative rep3 GSM4146628   source name:Tgkrt4:GFP embryos|age:4 somite stage|gfp:negative|tissue:non periderm GFP negative rep3 Sequencing reads were trimmed with Trimmomatic 0.35. Trimmed paired reads were pseudoaligned and quantified with kallisto v0.41; default parameters The output datasets from kallisto were normalized and compared using the sleuth program Genome build: danRer10 Supplementary files format and content: TPM.csv kallisto abundance.tsv Tgkrt4:GFP embryos FACS sort GFP positive and GFP negative cells Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer’s instructions.   age:4 somite stage|gfp:negative|tissue:non periderm GSM4146628 GSM4146628: GFP negative rep3; Danio rerio; RNA Seq GSM4146628   1 Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer's instructions. GEO Accession:GSM4146628 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP229597     noGFP_3_1.fastq.gz noGFP_3_2.fastq.gz fastq fastq 7881357168.0 51851034.0 GSM4146628 r1 0:76 1:76 A:2071239433;C:1863550437;G:1882684630;T:2062940287;N:942381 76 76     2071239433 1863550437 1882684630 2062940287 942381 SRX7130061 SRS5639405 SRA994593 GEO Anatomy and Cell Biology, University of Iowa 2 0.91729 0.91789 0.07407 0.07433 0.73417 0.74251 0.46769 0.46379 76 76 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-11-01 Segmentation Embryo Embryo Imprecise All anatomical structures
55475 55475 SRR10434087 SRX7130060 SRS5639404 SRP229597 PRJNA589032 mRNA profile of zebrafish periderm at 4 somite stage GSE139808 Transcriptome Analysis In order to compare the transcriptome and tissue specific nucleosome free regions of zebrafish periderm cells at 4 somite stage we isolated the RNA from sorted GFP positive cells of Tgkrt4:GFP embryos and perform low input RNA seq. This study revealed periderm specific transcriptome at 4 somite stage. Moreover comparing with ATAC seq from the same tissue we confirmed the correlation between gene expression and nearby chromatin accessibility. Overall design: GFP positive embryos were harvested from three independent incross of Tgkrt4:GFP. Embryos were dissociated and sorted with FACS. For each batch 2000 GFP positive and 2000 GFP negative cells were collected and subjected to RNA seq. parent bioproject:PRJNA589023 pubmed:32031521   GFP negative rep2 GSM4146627   source name:Tgkrt4:GFP embryos|age:4 somite stage|gfp:negative|tissue:non periderm GFP negative rep2 Sequencing reads were trimmed with Trimmomatic 0.35. Trimmed paired reads were pseudoaligned and quantified with kallisto v0.41; default parameters The output datasets from kallisto were normalized and compared using the sleuth program Genome build: danRer10 Supplementary files format and content: TPM.csv kallisto abundance.tsv Tgkrt4:GFP embryos FACS sort GFP positive and GFP negative cells Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer’s instructions.   age:4 somite stage|gfp:negative|tissue:non periderm GSM4146627 GSM4146627: GFP negative rep2; Danio rerio; RNA Seq GSM4146627   1 Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer's instructions. GEO Accession:GSM4146627 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP229597     noGFP_2_1.fastq.gz noGFP_2_2.fastq.gz fastq fastq 7242462560.0 47647780.0 GSM4146627 r1 0:76 1:76 A:1908219526;C:1706945798;G:1725605343;T:1900836812;N:855081 76 76     1908219526 1706945798 1725605343 1900836812 855081 SRX7130060 SRS5639404 SRA994593 GEO Anatomy and Cell Biology, University of Iowa 2 0.91551 0.91784 0.0763 0.07656 0.73271 0.74079 0.46415 0.4625 76 76 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-11-01 Segmentation Embryo Embryo Imprecise All anatomical structures
55476 55476 SRR10434086 SRX7130059 SRS5639403 SRP229597 PRJNA589032 mRNA profile of zebrafish periderm at 4 somite stage GSE139808 Transcriptome Analysis In order to compare the transcriptome and tissue specific nucleosome free regions of zebrafish periderm cells at 4 somite stage we isolated the RNA from sorted GFP positive cells of Tgkrt4:GFP embryos and perform low input RNA seq. This study revealed periderm specific transcriptome at 4 somite stage. Moreover comparing with ATAC seq from the same tissue we confirmed the correlation between gene expression and nearby chromatin accessibility. Overall design: GFP positive embryos were harvested from three independent incross of Tgkrt4:GFP. Embryos were dissociated and sorted with FACS. For each batch 2000 GFP positive and 2000 GFP negative cells were collected and subjected to RNA seq. parent bioproject:PRJNA589023 pubmed:32031521   GFP negative rep1 GSM4146626   source name:Tgkrt4:GFP embryos|age:4 somite stage|gfp:negative|tissue:non periderm GFP negative rep1 Sequencing reads were trimmed with Trimmomatic 0.35. Trimmed paired reads were pseudoaligned and quantified with kallisto v0.41; default parameters The output datasets from kallisto were normalized and compared using the sleuth program Genome build: danRer10 Supplementary files format and content: TPM.csv kallisto abundance.tsv Tgkrt4:GFP embryos FACS sort GFP positive and GFP negative cells Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer’s instructions.   age:4 somite stage|gfp:negative|tissue:non periderm GSM4146626 GSM4146626: GFP negative rep1; Danio rerio; RNA Seq GSM4146626   1 Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer's instructions. GEO Accession:GSM4146626 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP229597     noGFP_1_1.fastq.gz noGFP_1_2.fastq.gz fastq fastq 8313427352.0 54693601.0 GSM4146626 r1 0:76 1:76 A:2199335377;C:1952449683;G:1973334233;T:2187324388;N:983671 76 76     2199335377 1952449683 1973334233 2187324388 983671 SRX7130059 SRS5639403 SRA994593 GEO Anatomy and Cell Biology, University of Iowa 2 0.91335 0.91601 0.07579 0.07633 0.73265 0.74152 0.4622 0.46392 76 76 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-11-01 Segmentation Embryo Embryo Imprecise All anatomical structures
55477 55477 SRR10434085 SRX7130058 SRS5639402 SRP229597 PRJNA589032 mRNA profile of zebrafish periderm at 4 somite stage GSE139808 Transcriptome Analysis In order to compare the transcriptome and tissue specific nucleosome free regions of zebrafish periderm cells at 4 somite stage we isolated the RNA from sorted GFP positive cells of Tgkrt4:GFP embryos and perform low input RNA seq. This study revealed periderm specific transcriptome at 4 somite stage. Moreover comparing with ATAC seq from the same tissue we confirmed the correlation between gene expression and nearby chromatin accessibility. Overall design: GFP positive embryos were harvested from three independent incross of Tgkrt4:GFP. Embryos were dissociated and sorted with FACS. For each batch 2000 GFP positive and 2000 GFP negative cells were collected and subjected to RNA seq. parent bioproject:PRJNA589023 pubmed:32031521   GFP positive rep3 GSM4146625   source name:Tgkrt4:GFP embryos|age:4 somite stage|gfp:positive|tissue:periderm GFP positive rep3 Sequencing reads were trimmed with Trimmomatic 0.35. Trimmed paired reads were pseudoaligned and quantified with kallisto v0.41; default parameters The output datasets from kallisto were normalized and compared using the sleuth program Genome build: danRer10 Supplementary files format and content: TPM.csv kallisto abundance.tsv Tgkrt4:GFP embryos FACS sort GFP positive and GFP negative cells Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer’s instructions.   age:4 somite stage|gfp:positive|tissue:periderm GSM4146625 GSM4146625: GFP positive rep3; Danio rerio; RNA Seq GSM4146625   1 Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer's instructions. GEO Accession:GSM4146625 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP229597     GFP_3_1.fastq.gz GFP_3_2.fastq.gz fastq fastq 8502781808.0 55939354.0 GSM4146625 r1 0:76 1:76 A:2271615715;C:1982612632;G:1995770434;T:2251778240;N:1004787 76 76     2271615715 1982612632 1995770434 2251778240 1004787 SRX7130058 SRS5639402 SRA994593 GEO Anatomy and Cell Biology, University of Iowa 2 0.91393 0.91583 0.08066 0.08078 0.72496 0.7358 0.46199 0.46349 76 76 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-11-01 Segmentation Embryo Embryo Imprecise All anatomical structures
55478 55478 SRR10434084 SRX7130057 SRS5639401 SRP229597 PRJNA589032 mRNA profile of zebrafish periderm at 4 somite stage GSE139808 Transcriptome Analysis In order to compare the transcriptome and tissue specific nucleosome free regions of zebrafish periderm cells at 4 somite stage we isolated the RNA from sorted GFP positive cells of Tgkrt4:GFP embryos and perform low input RNA seq. This study revealed periderm specific transcriptome at 4 somite stage. Moreover comparing with ATAC seq from the same tissue we confirmed the correlation between gene expression and nearby chromatin accessibility. Overall design: GFP positive embryos were harvested from three independent incross of Tgkrt4:GFP. Embryos were dissociated and sorted with FACS. For each batch 2000 GFP positive and 2000 GFP negative cells were collected and subjected to RNA seq. parent bioproject:PRJNA589023 pubmed:32031521   GFP positive rep2 GSM4146624   source name:Tgkrt4:GFP embryos|age:4 somite stage|gfp:positive|tissue:periderm GFP positive rep2 Sequencing reads were trimmed with Trimmomatic 0.35. Trimmed paired reads were pseudoaligned and quantified with kallisto v0.41; default parameters The output datasets from kallisto were normalized and compared using the sleuth program Genome build: danRer10 Supplementary files format and content: TPM.csv kallisto abundance.tsv Tgkrt4:GFP embryos FACS sort GFP positive and GFP negative cells Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer’s instructions.   age:4 somite stage|gfp:positive|tissue:periderm GSM4146624 GSM4146624: GFP positive rep2; Danio rerio; RNA Seq GSM4146624   1 Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer's instructions. GEO Accession:GSM4146624 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP229597     GFP_2_1.fastq.gz GFP_2_2.fastq.gz fastq fastq 7348275232.0 48343916.0 GSM4146624 r1 0:76 1:76 A:1973611164;C:1698674270;G:1715303815;T:1959814356;N:871627 76 76     1973611164 1698674270 1715303815 1959814356 871627 SRX7130057 SRS5639401 SRA994593 GEO Anatomy and Cell Biology, University of Iowa 2 0.91471 0.91669 0.08005 0.0794 0.7261 0.73598 0.46042 0.46406 76 76 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-11-01 Segmentation Embryo Embryo Imprecise All anatomical structures
55479 55479 SRR10434083 SRX7130056 SRS5639400 SRP229597 PRJNA589032 mRNA profile of zebrafish periderm at 4 somite stage GSE139808 Transcriptome Analysis In order to compare the transcriptome and tissue specific nucleosome free regions of zebrafish periderm cells at 4 somite stage we isolated the RNA from sorted GFP positive cells of Tgkrt4:GFP embryos and perform low input RNA seq. This study revealed periderm specific transcriptome at 4 somite stage. Moreover comparing with ATAC seq from the same tissue we confirmed the correlation between gene expression and nearby chromatin accessibility. Overall design: GFP positive embryos were harvested from three independent incross of Tgkrt4:GFP. Embryos were dissociated and sorted with FACS. For each batch 2000 GFP positive and 2000 GFP negative cells were collected and subjected to RNA seq. parent bioproject:PRJNA589023 pubmed:32031521   GFP positive rep1 GSM4146623   source name:Tgkrt4:GFP embryos|age:4 somite stage|gfp:positive|tissue:periderm GFP positive rep1 Sequencing reads were trimmed with Trimmomatic 0.35. Trimmed paired reads were pseudoaligned and quantified with kallisto v0.41; default parameters The output datasets from kallisto were normalized and compared using the sleuth program Genome build: danRer10 Supplementary files format and content: TPM.csv kallisto abundance.tsv Tgkrt4:GFP embryos FACS sort GFP positive and GFP negative cells Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer’s instructions.   age:4 somite stage|gfp:positive|tissue:periderm GSM4146623 GSM4146623: GFP positive rep1; Danio rerio; RNA Seq GSM4146623   1 Total RNA was extracted from the sorted cells using the RNAqueous® Total RNA Isolation Kit Ambion Foster City CA and treated with Turbo DNase I Ambion Austin TX to remove residual genomic DNA. The treated RNA was then purified and concentrated using the RNA Clean & ConcentratorTM 5 Kit Zymo Research Irvine CA. 1 ug of RNA was subjected to first strand cDNA synthesis and cDNA amplification using the SMART Seq® v4 Ultra® Low Input RNA Kit Takara Bio Kusatsu Shiga Japan. Purified cDNA was quantified using Qubit and for each library 150 pg cDNA was used as input with the Nextera XT DNA Sample Preparation Kit Illumina San Diego CA following the manufacturer's instructions. GEO Accession:GSM4146623 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP229597     GFP_1_1.fastq.gz GFP_1_2.fastq.gz fastq fastq 9022496256.0 59358528.0 GSM4146623 r1 0:76 1:76 A:2432258451;C:2072280272;G:2093532167;T:2423357660;N:1067706 76 76     2432258451 2072280272 2093532167 2423357660 1067706 SRX7130056 SRS5639400 SRA994593 GEO Anatomy and Cell Biology, University of Iowa 2 0.91017 0.91402 0.08201 0.08274 0.72865 0.73882 0.46136 0.4624 76 76 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified nextera sc single_cell_plate smartseq   United States 2019-11-01 Segmentation Embryo Embryo Imprecise All anatomical structures
68802 68802 SRR18192285 SRX14338886 SRS12152815 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 18 GSM5929605   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 18 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929605 GSM5929605: ventral EC 21hpf 18; Danio rerio; RNA Seq GSM5929605 r1 GSM5929605 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_18_FKDL190751240-1a-N705-N505_1.fq.gz zsz_RNAseq-Ventral_18_FKDL190751240-1a-N705-N505_2.fq.gz fastq fastq 1058538600.0 3528462.0 GSM5929605 r1 0:150 1:150 A:285217036;C:228726389;G:249376358;T:295208341;N:10476 150 150     285217036 228726389 249376358 295208341 10476 SRX14338886 SRS12152815     Wen's lab, LIFS, HKUST 2 0.8351 0.83673 0.26078 0.26108 0.88075 0.88063 0.52695 0.52551 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68803 68803 SRR18192286 SRX14338885 SRS12152814 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 17 GSM5929604   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 17 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929604 GSM5929604: ventral EC 21hpf 17; Danio rerio; RNA Seq GSM5929604 r1 GSM5929604 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_17_FKDL190751240-1a-N705-N504_1.fq.gz zsz_RNAseq-Ventral_17_FKDL190751240-1a-N705-N504_2.fq.gz fastq fastq 1710113700.0 5700379.0 GSM5929604 r1 0:150 1:150 A:456993578;C:374801345;G:404311166;T:473990816;N:16795 150 150     456993578 374801345 404311166 473990816 16795 SRX14338885 SRS12152814     Wen's lab, LIFS, HKUST 2 0.8705 0.87468 0.12928 0.13 0.85236 0.85027 0.51504 0.52028 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68804 68804 SRR18192287 SRX14338884 SRS12152813 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 16 GSM5929603   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 16 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929603 GSM5929603: ventral EC 21hpf 16; Danio rerio; RNA Seq GSM5929603 r1 GSM5929603 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_16_FKDL190751240-1a-N705-N503_1.fq.gz zsz_RNAseq-Ventral_16_FKDL190751240-1a-N705-N503_2.fq.gz fastq fastq 2135517900.0 7118393.0 GSM5929603 r1 0:150 1:150 A:571832219;C:435335243;G:553151794;T:575177473;N:21171 150 150     571832219 435335243 553151794 575177473 21171 SRX14338884 SRS12152813     Wen's lab, LIFS, HKUST 2 0.81782 0.82162 0.19664 0.19844 0.90258 0.9021 0.54734 0.5485 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68805 68805 SRR18192288 SRX14338883 SRS12152812 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 15 GSM5929602   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 15 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929602 GSM5929602: ventral EC 21hpf 15; Danio rerio; RNA Seq GSM5929602 r1 GSM5929602 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_15_FKDL190751240-1a-N705-N502_1.fq.gz zsz_RNAseq-Ventral_15_FKDL190751240-1a-N705-N502_2.fq.gz fastq fastq 3885311700.0 12951039.0 GSM5929602 r1 0:150 1:150 A:1010757981;C:831053908;G:1024608296;T:1018853576;N:37939 150 150     1010757981 831053908 1024608296 1018853576 37939 SRX14338883 SRS12152812     Wen's lab, LIFS, HKUST 2 0.87023 0.8742 0.12367 0.12442 0.8955 0.89566 0.50086 0.50105 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68806 68806 SRR18192289 SRX14338882 SRS12152811 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 14 GSM5929601   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 14 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929601 GSM5929601: ventral EC 21hpf 14; Danio rerio; RNA Seq GSM5929601 r1 GSM5929601 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_14_FKDL190751240-1a-N705-N501_1.fq.gz zsz_RNAseq-Ventral_14_FKDL190751240-1a-N705-N501_2.fq.gz fastq fastq 1414279800.0 4714266.0 GSM5929601 r1 0:150 1:150 A:367480462;C:303466342;G:363199319;T:380119999;N:13678 150 150     367480462 303466342 363199319 380119999 13678 SRX14338882 SRS12152811     Wen's lab, LIFS, HKUST 2 0.88322 0.88355 0.14697 0.14777 0.87698 0.87495 0.41966 0.49893 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68807 68807 SRR18192290 SRX14338881 SRS12152810 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 13 GSM5929600   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 13 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929600 GSM5929600: ventral EC 21hpf 13; Danio rerio; RNA Seq GSM5929600 r1 GSM5929600 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_13_FKDL190751240-1a-N704-N508_1.fq.gz zsz_RNAseq-Ventral_13_FKDL190751240-1a-N704-N508_2.fq.gz fastq fastq 1452180000.0 4840600.0 GSM5929600 r1 0:150 1:150 A:375352428;C:312937004;G:373721430;T:390154997;N:14141 150 150     375352428 312937004 373721430 390154997 14141 SRX14338881 SRS12152810     Wen's lab, LIFS, HKUST 2 0.87731 0.8773 0.16356 0.16442 0.85531 0.85372 0.44481 0.53329 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68808 68808 SRR18192291 SRX14338880 SRS12152809 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 12 GSM5929599   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 12 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929599 GSM5929599: ventral EC 21hpf 12; Danio rerio; RNA Seq GSM5929599 r1 GSM5929599 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_12_FKDL190751240-1a-N704-N507_1.fq.gz zsz_RNAseq-Ventral_12_FKDL190751240-1a-N704-N507_2.fq.gz fastq fastq 197506200.0 658354.0 GSM5929599 r1 0:150 1:150 A:55193587;C:39652606;G:46184943;T:56473475;N:1589 150 150     55193587 39652606 46184943 56473475 1589 SRX14338880 SRS12152809     Wen's lab, LIFS, HKUST 2 0.54767 0.56916 0.16484 0.17354 0.92462 0.92145 0.59396 0.61207 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68809 68809 SRR18192292 SRX14338879 SRS12152808 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 11 GSM5929598   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 11 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929598 GSM5929598: ventral EC 21hpf 11; Danio rerio; RNA Seq GSM5929598 r1 GSM5929598 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_11_FKDL190751240-1a-N704-N506_1.fq.gz zsz_RNAseq-Ventral_11_FKDL190751240-1a-N704-N506_2.fq.gz fastq fastq 2819811300.0 9399371.0 GSM5929598 r1 0:150 1:150 A:743219116;C:598297990;G:707979206;T:770286294;N:28694 150 150     743219116 598297990 707979206 770286294 28694 SRX14338879 SRS12152808     Wen's lab, LIFS, HKUST 2 0.85748 0.86013 0.14091 0.14141 0.86208 0.86156 0.43221 0.51466 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68810 68810 SRR18192293 SRX14338878 SRS12152807 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 10 GSM5929597   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 10 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929597 GSM5929597: ventral EC 21hpf 10; Danio rerio; RNA Seq GSM5929597 r1 GSM5929597 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_10_FKDL190751240-1a-N704-N505_1.fq.gz zsz_RNAseq-Ventral_10_FKDL190751240-1a-N704-N505_2.fq.gz fastq fastq 1576310400.0 5254368.0 GSM5929597 r1 0:150 1:150 A:410912154;C:347293007;G:391583898;T:426506333;N:15008 150 150     410912154 347293007 391583898 426506333 15008 SRX14338878 SRS12152807     Wen's lab, LIFS, HKUST 2 0.84499 0.84589 0.15162 0.15228 0.86196 0.86056 0.53985 0.55012 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68811 68811 SRR18192294 SRX14338877 SRS12152806 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 9 GSM5929596   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 9 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929596 GSM5929596: ventral EC 21hpf 9; Danio rerio; RNA Seq GSM5929596 r1 GSM5929596 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_9_FKDL190751240-1a-N704-N504_1.fq.gz zsz_RNAseq-Ventral_9_FKDL190751240-1a-N704-N504_2.fq.gz fastq fastq 1980675000.0 6602250.0 GSM5929596 r1 0:150 1:150 A:536215524;C:426395646;G:466508618;T:551535351;N:19861 150 150     536215524 426395646 466508618 551535351 19861 SRX14338877 SRS12152806     Wen's lab, LIFS, HKUST 2 0.83681 0.83934 0.19282 0.19391 0.88051 0.8801 0.54882 0.55989 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68812 68812 SRR18192295 SRX14338876 SRS12152805 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 8 GSM5929595   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 8 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929595 GSM5929595: ventral EC 21hpf 8; Danio rerio; RNA Seq GSM5929595 r1 GSM5929595 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_8_FKDL190751240-1a-N704-N503_1.fq.gz zsz_RNAseq-Ventral_8_FKDL190751240-1a-N704-N503_2.fq.gz fastq fastq 2005588800.0 6685296.0 GSM5929595 r1 0:150 1:150 A:524503806;C:412556232;G:540908686;T:527599906;N:20170 150 150     524503806 412556232 540908686 527599906 20170 SRX14338876 SRS12152805     Wen's lab, LIFS, HKUST 2 0.80248 0.80782 0.16645 0.16694 0.86078 0.86064 0.50743 0.51068 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68813 68813 SRR18192296 SRX14338875 SRS12152804 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 7 GSM5929594   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 7 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929594 GSM5929594: ventral EC 21hpf 7; Danio rerio; RNA Seq GSM5929594 r1 GSM5929594 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_7_FKDL190751240-1a-N704-N502_1.fq.gz zsz_RNAseq-Ventral_7_FKDL190751240-1a-N704-N502_2.fq.gz fastq fastq 788933400.0 2629778.0 GSM5929594 r1 0:150 1:150 A:216991096;C:163431009;G:190917976;T:217585421;N:7898 150 150     216991096 163431009 190917976 217585421 7898 SRX14338875 SRS12152804     Wen's lab, LIFS, HKUST 2 0.83789 0.83907 0.25103 0.25239 0.89455 0.89469 0.54039 0.52841 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68814 68814 SRR18192297 SRX14338874 SRS12152803 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 6 GSM5929593   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 6 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929593 GSM5929593: ventral EC 21hpf 6; Danio rerio; RNA Seq GSM5929593 r1 GSM5929593 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_6_FKDL190751240-1a-N704-N501_1.fq.gz zsz_RNAseq-Ventral_6_FKDL190751240-1a-N704-N501_2.fq.gz fastq fastq 450110400.0 1500368.0 GSM5929593 r1 0:150 1:150 A:126821493;C:94637888;G:99950745;T:128696606;N:3668 150 150     126821493 94637888 99950745 128696606 3668 SRX14338874 SRS12152803     Wen's lab, LIFS, HKUST 2 0.66559 0.66089 0.13677 0.1407 0.88499 0.88099 0.54848 0.43228 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68815 68815 SRR18192298 SRX14338873 SRS12152802 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 5 GSM5929592   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 5 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929592 GSM5929592: ventral EC 21hpf 5; Danio rerio; RNA Seq GSM5929592 r1 GSM5929592 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_5_FKDL190751240-1a-N703-N508_1.fq.gz zsz_RNAseq-Ventral_5_FKDL190751240-1a-N703-N508_2.fq.gz fastq fastq 1932989400.0 6443298.0 GSM5929592 r1 0:150 1:150 A:498852833;C:411538343;G:530884169;T:491695543;N:18512 150 150     498852833 411538343 530884169 491695543 18512 SRX14338873 SRS12152802     Wen's lab, LIFS, HKUST 2 0.84408 0.85118 0.07703 0.07828 0.87485 0.87476 0.54748 0.54046 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68816 68816 SRR18192299 SRX14338872 SRS12152801 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 4 GSM5929591   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 4 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929591 GSM5929591: ventral EC 21hpf 4; Danio rerio; RNA Seq GSM5929591 r1 GSM5929591 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_4_FKDL190751240-1a-N703-N507_1.fq.gz zsz_RNAseq-Ventral_4_FKDL190751240-1a-N703-N507_2.fq.gz fastq fastq 1878780300.0 6262601.0 GSM5929591 r1 0:150 1:150 A:478553640;C:410195248;G:508351905;T:481660592;N:18915 150 150     478553640 410195248 508351905 481660592 18915 SRX14338872 SRS12152801     Wen's lab, LIFS, HKUST 2 0.86028 0.86863 0.09492 0.09584 0.86324 0.86283 0.55955 0.55922 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68817 68817 SRR18192300 SRX14338871 SRS12152800 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 3 GSM5929590   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 3 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929590 GSM5929590: ventral EC 21hpf 3; Danio rerio; RNA Seq GSM5929590 r1 GSM5929590 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_3_FKDL190751240-1a-N703-N506_1.fq.gz zsz_RNAseq-Ventral_3_FKDL190751240-1a-N703-N506_2.fq.gz fastq fastq 1015675200.0 3385584.0 GSM5929590 r1 0:150 1:150 A:268281264;C:217586968;G:263830356;T:265966204;N:10408 150 150     268281264 217586968 263830356 265966204 10408 SRX14338871 SRS12152800     Wen's lab, LIFS, HKUST 2 0.81737 0.82273 0.10314 0.10376 0.9053 0.90542 0.56877 0.57074 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68818 68818 SRR18192301 SRX14338870 SRS12152799 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 2 GSM5929589   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 2 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929589 GSM5929589: ventral EC 21hpf 2; Danio rerio; RNA Seq GSM5929589 r1 GSM5929589 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_2_FKDL190751240-1a-N703-N505_1.fq.gz zsz_RNAseq-Ventral_2_FKDL190751240-1a-N703-N505_2.fq.gz fastq fastq 984832500.0 3282775.0 GSM5929589 r1 0:150 1:150 A:262133870;C:213059820;G:253998346;T:255630407;N:10057 150 150     262133870 213059820 253998346 255630407 10057 SRX14338870 SRS12152799     Wen's lab, LIFS, HKUST 2 0.81688 0.82614 0.09728 0.09853 0.89656 0.89611 0.56514 0.56357 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68819 68819 SRR18192302 SRX14338869 SRS12152798 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   ventral EC 21hpf 1 GSM5929588   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs ventral EC 21hpf 1 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA floor|cell type:endothelial cells ECs GSM5929588 GSM5929588: ventral EC 21hpf 1; Danio rerio; RNA Seq GSM5929588 r1 GSM5929588 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Ventral_1_FKDL190751240-1a-N703-N504_1.fq.gz zsz_RNAseq-Ventral_1_FKDL190751240-1a-N703-N504_2.fq.gz fastq fastq 1030305900.0 3434353.0 GSM5929588 r1 0:150 1:150 A:273847380;C:230836779;G:249559051;T:276052448;N:10242 150 150     273847380 230836779 249559051 276052448 10242 SRX14338869 SRS12152798     Wen's lab, LIFS, HKUST 2 0.90435 0.90889 0.08763 0.08824 0.83319 0.83351 0.52714 0.53055 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68820 68820 SRR18192303 SRX14338868 SRS12152797 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 18 GSM5929587   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 18 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929587 GSM5929587: dorsal EC 21hpf 18; Danio rerio; RNA Seq GSM5929587 r1 GSM5929587 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_18_FKDL190751240-1a-N703-N502_1.fq.gz zsz_RNAseq-Dorsal_18_FKDL190751240-1a-N703-N502_2.fq.gz fastq fastq 3061497900.0 10204993.0 GSM5929587 r1 0:150 1:150 A:841826817;C:618508714;G:779078448;T:822053769;N:30152 150 150     841826817 618508714 779078448 822053769 30152 SRX14338868 SRS12152797     Wen's lab, LIFS, HKUST 2 0.86141 0.86592 0.16355 0.16475 0.90321 0.90335 0.54328 0.5446 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68821 68821 SRR18192304 SRX14338867 SRS12152796 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 17 GSM5929586   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 17 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929586 GSM5929586: dorsal EC 21hpf 17; Danio rerio; RNA Seq GSM5929586 r1 GSM5929586 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_17_FKDL190751240-1a-N703-N501_1.fq.gz zsz_RNAseq-Dorsal_17_FKDL190751240-1a-N703-N501_2.fq.gz fastq fastq 3011917200.0 10039724.0 GSM5929586 r1 0:150 1:150 A:796006953;C:646449934;G:766849838;T:802581204;N:29271 150 150     796006953 646449934 766849838 802581204 29271 SRX14338867 SRS12152796     Wen's lab, LIFS, HKUST 2 0.85453 0.85849 0.1385 0.13969 0.87026 0.86918 0.42229 0.51272 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68822 68822 SRR18192305 SRX14338866 SRS12152795 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 16 GSM5929585   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 16 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929585 GSM5929585: dorsal EC 21hpf 16; Danio rerio; RNA Seq GSM5929585 r1 GSM5929585 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_16_FKDL190751240-1a-N702-N508_1.fq.gz zsz_RNAseq-Dorsal_16_FKDL190751240-1a-N702-N508_2.fq.gz fastq fastq 1370512800.0 4568376.0 GSM5929585 r1 0:150 1:150 A:372445736;C:279457475;G:338671006;T:379925174;N:13409 150 150     372445736 279457475 338671006 379925174 13409 SRX14338866 SRS12152795     Wen's lab, LIFS, HKUST 2 0.85206 0.85292 0.21543 0.21661 0.8994 0.89826 0.51979 0.4287 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68823 68823 SRR18192306 SRX14338865 SRS12152794 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 15 GSM5929584   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 15 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929584 GSM5929584: dorsal EC 21hpf 15; Danio rerio; RNA Seq GSM5929584 r1 GSM5929584 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_15_FKDL190751240-1a-N702-N507_1.fq.gz zsz_RNAseq-Dorsal_15_FKDL190751240-1a-N702-N507_2.fq.gz fastq fastq 1425857100.0 4752857.0 GSM5929584 r1 0:150 1:150 A:380566894;C:299416965;G:356418162;T:389440755;N:14324 150 150     380566894 299416965 356418162 389440755 14324 SRX14338865 SRS12152794     Wen's lab, LIFS, HKUST 2 0.84839 0.856 0.11828 0.11988 0.91332 0.9125 0.55622 0.55424 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68824 68824 SRR18192307 SRX14338864 SRS12152793 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 14 GSM5929583   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 14 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929583 GSM5929583: dorsal EC 21hpf 14; Danio rerio; RNA Seq GSM5929583 r1 GSM5929583 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_14_FKDL190751240-1a-N702-N506_1.fq.gz zsz_RNAseq-Dorsal_14_FKDL190751240-1a-N702-N506_2.fq.gz fastq fastq 1341641400.0 4472138.0 GSM5929583 r1 0:150 1:150 A:352469267;C:286189242;G:335344641;T:367624807;N:13443 150 150     352469267 286189242 335344641 367624807 13443 SRX14338864 SRS12152793     Wen's lab, LIFS, HKUST 2 0.90133 0.90251 0.15458 0.15541 0.8394 0.83926 0.5369 0.53853 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68825 68825 SRR18192308 SRX14338863 SRS12152792 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 13 GSM5929582   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 13 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929582 GSM5929582: dorsal EC 21hpf 13; Danio rerio; RNA Seq GSM5929582 r1 GSM5929582 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_13_FKDL190751240-1a-N702-N505_1.fq.gz zsz_RNAseq-Dorsal_13_FKDL190751240-1a-N702-N505_2.fq.gz fastq fastq 514111800.0 1713706.0 GSM5929582 r1 0:150 1:150 A:139200488;C:110644075;G:120719381;T:143542952;N:4904 150 150     139200488 110644075 120719381 143542952 4904 SRX14338863 SRS12152792     Wen's lab, LIFS, HKUST 2 0.85117 0.8533 0.15163 0.15242 0.85863 0.85882 0.43388 0.44077 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68826 68826 SRR18192309 SRX14338862 SRS12152791 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 12 GSM5929581   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 12 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929581 GSM5929581: dorsal EC 21hpf 12; Danio rerio; RNA Seq GSM5929581 r1 GSM5929581 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_12_FKDL190751240-1a-N702-N504_1.fq.gz zsz_RNAseq-Dorsal_12_FKDL190751240-1a-N702-N504_2.fq.gz fastq fastq 1851950100.0 6173167.0 GSM5929581 r1 0:150 1:150 A:509560243;C:394907027;G:434327069;T:513137188;N:18573 150 150     509560243 394907027 434327069 513137188 18573 SRX14338862 SRS12152791     Wen's lab, LIFS, HKUST 2 0.79607 0.80051 0.08178 0.08199 0.9161 0.91563 0.47644 0.46947 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68827 68827 SRR18192310 SRX14338861 SRS12152790 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 11 GSM5929580   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 11 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929580 GSM5929580: dorsal EC 21hpf 11; Danio rerio; RNA Seq GSM5929580 r1 GSM5929580 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_11_FKDL190751240-1a-N702-N503_1.fq.gz zsz_RNAseq-Dorsal_11_FKDL190751240-1a-N702-N503_2.fq.gz fastq fastq 465059700.0 1550199.0 GSM5929580 r1 0:150 1:150 A:123918130;C:95363604;G:123048161;T:122725418;N:4387 150 150     123918130 95363604 123048161 122725418 4387 SRX14338861 SRS12152790     Wen's lab, LIFS, HKUST 2 0.83887 0.84236 0.07473 0.0754 0.92115 0.9209 0.46874 0.46289 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68828 68828 SRR18192311 SRX14338860 SRS12152789 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 10 GSM5929579   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 10 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929579 GSM5929579: dorsal EC 21hpf 10; Danio rerio; RNA Seq GSM5929579 r1 GSM5929579 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_10_FKDL190751240-1a-N702-N502_1.fq.gz zsz_RNAseq-Dorsal_10_FKDL190751240-1a-N702-N502_2.fq.gz fastq fastq 188240400.0 627468.0 GSM5929579 r1 0:150 1:150 A:50708735;C:38450113;G:49057806;T:50021859;N:1887 150 150     50708735 38450113 49057806 50021859 1887 SRX14338860 SRS12152789     Wen's lab, LIFS, HKUST 2 0.82852 0.83125 0.08228 0.08313 0.91981 0.91932 0.47584 0.47283 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68829 68829 SRR18192312 SRX14338859 SRS12152788 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 9 GSM5929578   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 9 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929578 GSM5929578: dorsal EC 21hpf 9; Danio rerio; RNA Seq GSM5929578 r1 GSM5929578 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_9_FKDL190751240-1a-N702-N501_1.fq.gz zsz_RNAseq-Dorsal_9_FKDL190751240-1a-N702-N501_2.fq.gz fastq fastq 127740000.0 425800.0 GSM5929578 r1 0:150 1:150 A:34591922;C:26171242;G:31577043;T:35398589;N:1204 150 150     34591922 26171242 31577043 35398589 1204 SRX14338859 SRS12152788     Wen's lab, LIFS, HKUST 2 0.88617 0.88943 0.20527 0.20926 0.92342 0.92153 0.57721 0.58247 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68830 68830 SRR18192313 SRX14338858 SRS12152787 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 8 GSM5929577   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 8 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929577 GSM5929577: dorsal EC 21hpf 8; Danio rerio; RNA Seq GSM5929577 r1 GSM5929577 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_8_FKDL190751240-1a-N701-N508_1.fq.gz zsz_RNAseq-Dorsal_8_FKDL190751240-1a-N701-N508_2.fq.gz fastq fastq 825913200.0 2753044.0 GSM5929577 r1 0:150 1:150 A:227718140;C:172715023;G:195047159;T:230425305;N:7573 150 150     227718140 172715023 195047159 230425305 7573 SRX14338858 SRS12152787     Wen's lab, LIFS, HKUST 2 0.88714 0.88544 0.13726 0.13867 0.87884 0.87691 0.52543 0.51995 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68831 68831 SRR18192314 SRX14338857 SRS12152786 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 7 GSM5929576   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 7 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929576 GSM5929576: dorsal EC 21hpf 7; Danio rerio; RNA Seq GSM5929576 r1 GSM5929576 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_7_FKDL190751240-1a-N701-N507_1.fq.gz zsz_RNAseq-Dorsal_7_FKDL190751240-1a-N701-N507_2.fq.gz fastq fastq 2514663900.0 8382213.0 GSM5929576 r1 0:150 1:150 A:684885317;C:530845141;G:596157276;T:702750812;N:25354 150 150     684885317 530845141 596157276 702750812 25354 SRX14338857 SRS12152786     Wen's lab, LIFS, HKUST 2 0.90437 0.90564 0.33352 0.33483 0.88868 0.88791 0.62156 0.61061 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68832 68832 SRR18192315 SRX14338856 SRS12152785 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 6 GSM5929575   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 6 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929575 GSM5929575: dorsal EC 21hpf 6; Danio rerio; RNA Seq GSM5929575 r1 GSM5929575 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_6_FKDL190751240-1a-N701-N506_1.fq.gz zsz_RNAseq-Dorsal_6_FKDL190751240-1a-N701-N506_2.fq.gz fastq fastq 1932339000.0 6441130.0 GSM5929575 r1 0:150 1:150 A:530283479;C:405407998;G:458622469;T:538005738;N:19316 150 150     530283479 405407998 458622469 538005738 19316 SRX14338856 SRS12152785     Wen's lab, LIFS, HKUST 2 0.87219 0.87314 0.1397 0.14049 0.90256 0.90246 0.53019 0.52081 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68833 68833 SRR18192316 SRX14338855 SRS12152784 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 5 GSM5929574   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 5 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929574 GSM5929574: dorsal EC 21hpf 5; Danio rerio; RNA Seq GSM5929574 r1 GSM5929574 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_5_FKDL190751240-1a-N701-N505_1.fq.gz zsz_RNAseq-Dorsal_5_FKDL190751240-1a-N701-N505_2.fq.gz fastq fastq 250998000.0 836660.0 GSM5929574 r1 0:150 1:150 A:69694573;C:53729650;G:56820750;T:70750489;N:2538 150 150     69694573 53729650 56820750 70750489 2538 SRX14338855 SRS12152784     Wen's lab, LIFS, HKUST 2 0.87223 0.87083 0.14982 0.14954 0.8658 0.86551 0.53464 0.53124 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68834 68834 SRR18192317 SRX14338854 SRS12152783 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 4 GSM5929573   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 4 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929573 GSM5929573: dorsal EC 21hpf 4; Danio rerio; RNA Seq GSM5929573 r1 GSM5929573 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_4_FKDL190751240-1a-N701-N504_1.fq.gz zsz_RNAseq-Dorsal_4_FKDL190751240-1a-N701-N504_2.fq.gz fastq fastq 1815418200.0 6051394.0 GSM5929573 r1 0:150 1:150 A:512548347;C:380411599;G:403574055;T:518866610;N:17589 150 150     512548347 380411599 403574055 518866610 17589 SRX14338854 SRS12152783     Wen's lab, LIFS, HKUST 2 0.89228 0.89263 0.12677 0.12768 0.90524 0.90571 0.56202 0.56026 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68835 68835 SRR18192318 SRX14338853 SRS12152782 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 3 GSM5929572   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 3 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929572 GSM5929572: dorsal EC 21hpf 3; Danio rerio; RNA Seq GSM5929572 r1 GSM5929572 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_3_FKDL190751240-1a-N701-N503_1.fq.gz zsz_RNAseq-Dorsal_3_FKDL190751240-1a-N701-N503_2.fq.gz fastq fastq 3833578500.0 12778595.0 GSM5929572 r1 0:150 1:150 A:1024969861;C:818587907;G:970359067;T:1019622893;N:38772 150 150     1024969861 818587907 970359067 1019622893 38772 SRX14338853 SRS12152782     Wen's lab, LIFS, HKUST 2 0.76432 0.76237 0.06298 0.06367 0.93452 0.9344 0.48474 0.48285 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68836 68836 SRR18192319 SRX14338852 SRS12152781 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 2 GSM5929571   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 2 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929571 GSM5929571: dorsal EC 21hpf 2; Danio rerio; RNA Seq GSM5929571 r1 GSM5929571 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_2_FKDL190751240-1a-N701-N502_1.fq.gz zsz_RNAseq-Dorsal_2_FKDL190751240-1a-N701-N502_2.fq.gz fastq fastq 3680603400.0 12268678.0 GSM5929571 r1 0:150 1:150 A:991863514;C:757080877;G:947927995;T:983694701;N:36313 150 150     991863514 757080877 947927995 983694701 36313 SRX14338852 SRS12152781     Wen's lab, LIFS, HKUST 2 0.81803 0.81797 0.11433 0.11515 0.89183 0.89207 0.5414 0.53768 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
68837 68837 SRR18192320 SRX14338851 SRS12152780 SRP362184 PRJNA812001 scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish GSE197757 Transcriptome Analysis In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs   pubmed:35333649   dorsal EC 21hpf 1 GSM5929570   source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs dorsal EC 21hpf 1 Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample Trunk DA endothelium   Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs GSM5929570 GSM5929570: dorsal EC 21hpf 1; Danio rerio; RNA Seq GSM5929570 r1 GSM5929570 1 Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP362184   loader:fastq load.py zsz_RNAseq-Dorsal_1_FKDL190751240-1a-N701-N501_1.fq.gz zsz_RNAseq-Dorsal_1_FKDL190751240-1a-N701-N501_2.fq.gz fastq fastq 1591674900.0 5305583.0 GSM5929570 r1 0:150 1:150 A:445156133;C:336201938;G:359744664;T:450558818;N:13347 150 150     445156133 336201938 359744664 450558818 13347 SRX14338851 SRS12152780     Wen's lab, LIFS, HKUST 2 0.85257 0.85794 0.14033 0.14535 0.86371 0.86135 0.55057 0.55035 150 150 B B biological fallback assumption illumina hiseq_era full_length poly_a unknown sc single_cell_plate smartseq   China 2022-03-02 Segmentation Embryo Heart Cardiovascular System
69580 69580 SRR18927184 SRX15004844 SRS12753556 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 GSM6068604   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068604 GSM6068604: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3; Danio rerio; RNA Seq GSM6068604 r1 GSM6068604 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_03_S9_L001_R1_001.fastq.gz fastq 744134237.0 10221322.0 GSM6068604 r1 0:72.80 1:0 A:200415459;C:170890467;G:175699158;T:196451943;N:677210 72 0     200415459 170890467 175699158 196451943 677210 SRX15004844 SRS12753556 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93677   0.0458   0.76144   0.51338   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69581 69581 SRR18927185 SRX15004844 SRS12753556 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 GSM6068604   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068604 GSM6068604: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3; Danio rerio; RNA Seq GSM6068604 r1 GSM6068604 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_03_S9_L002_R1_001.fastq.gz fastq 713336563.0 9806369.0 GSM6068604 r2 0:72.74 1:0 A:192232089;C:164110978;G:167926911;T:188411430;N:655155 72 0     192232089 164110978 167926911 188411430 655155 SRX15004844 SRS12753556 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93575   0.0459   0.7628   0.52271   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69582 69582 SRR18927186 SRX15004844 SRS12753556 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 GSM6068604   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068604 GSM6068604: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3; Danio rerio; RNA Seq GSM6068604 r1 GSM6068604 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_03_S9_L003_R1_001.fastq.gz fastq 718617566.0 9871758.0 GSM6068604 r3 0:72.80 1:0 A:193895503;C:165112470;G:169254039;T:189730714;N:624840 72 0     193895503 165112470 169254039 189730714 624840 SRX15004844 SRS12753556 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.9355   0.04598   0.76459   0.5158   73   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69583 69583 SRR18927187 SRX15004844 SRS12753556 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 GSM6068604   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068604 GSM6068604: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 3; Danio rerio; RNA Seq GSM6068604 r1 GSM6068604 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_03_S9_L004_R1_001.fastq.gz fastq 727564590.0 9976511.0 GSM6068604 r4 0:72.93 1:0 A:196363760;C:167163486;G:171092104;T:192383180;N:562060 72 0     196363760 167163486 171092104 192383180 562060 SRX15004844 SRS12753556 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93595   0.04601   0.76353   0.51732   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69584 69584 SRR18927188 SRX15004843 SRS12753555 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 GSM6068603   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068603 GSM6068603: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2; Danio rerio; RNA Seq GSM6068603 r1 GSM6068603 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_02_S8_L001_R1_001.fastq.gz fastq 697802741.0 9548738.0 GSM6068603 r1 0:73.08 1:0 A:187922068;C:160061203;G:164649390;T:184626878;N:543202 73 0     187922068 160061203 164649390 184626878 543202 SRX15004843 SRS12753555 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93586   0.05129   0.76424   0.52169   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69585 69585 SRR18927189 SRX15004843 SRS12753555 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 GSM6068603   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068603 GSM6068603: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2; Danio rerio; RNA Seq GSM6068603 r1 GSM6068603 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_02_S8_L002_R1_001.fastq.gz fastq 662903444.0 9078930.0 GSM6068603 r2 0:73.02 1:0 A:178605669;C:152357709;G:156008633;T:175409889;N:521544 73 0     178605669 152357709 156008633 175409889 521544 SRX15004843 SRS12753555 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93653   0.05146   0.7628   0.51778   74   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69586 69586 SRR18927190 SRX15004843 SRS12753555 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 GSM6068603   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068603 GSM6068603: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2; Danio rerio; RNA Seq GSM6068603 r1 GSM6068603 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_02_S8_L003_R1_001.fastq.gz fastq 668311097.0 9143688.0 GSM6068603 r3 0:73.09 1:0 A:180289485;C:153373494;G:157331239;T:176839110;N:477769 73 0     180289485 153373494 157331239 176839110 477769 SRX15004843 SRS12753555 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93696   0.05225   0.7637   0.51732   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69587 69587 SRR18927191 SRX15004843 SRS12753555 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 GSM6068603   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068603 GSM6068603: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 2; Danio rerio; RNA Seq GSM6068603 r1 GSM6068603 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_02_S8_L004_R1_001.fastq.gz fastq 680968806.0 9296775.0 GSM6068603 r4 0:73.25 1:0 A:183838465;C:156195225;G:160056448;T:180449193;N:429475 73 0     183838465 156195225 160056448 180449193 429475 SRX15004843 SRS12753555 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93695   0.05036   0.76394   0.52148   55   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69588 69588 SRR18927192 SRX15004842 SRS12753554 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1 GSM6068602   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068602 GSM6068602: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1; Danio rerio; RNA Seq GSM6068602 r1 GSM6068602 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_01_S7_L001_R1_001.fastq.gz fastq 860623909.0 11793192.0 GSM6068602 r1 0:72.98 1:0 A:231785480;C:197544026;G:202920509;T:227621795;N:752099 72 0     231785480 197544026 202920509 227621795 752099 SRX15004842 SRS12753554 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93103   0.0562   0.76179   0.51243   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69589 69589 SRR18927193 SRX15004842 SRS12753554 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1 GSM6068602   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068602 GSM6068602: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1; Danio rerio; RNA Seq GSM6068602 r1 GSM6068602 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_01_S7_L002_R1_001.fastq.gz fastq 829335984.0 11372967.0 GSM6068602 r2 0:72.92 1:0 A:223480519;C:190755977;G:194990382;T:219387236;N:721870 72 0     223480519 190755977 194990382 219387236 721870 SRX15004842 SRS12753554 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93059   0.05558   0.76106   0.51174   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69590 69590 SRR18927194 SRX15004842 SRS12753554 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1 GSM6068602   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068602 GSM6068602: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1; Danio rerio; RNA Seq GSM6068602 r1 GSM6068602 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_01_S7_L003_R1_001.fastq.gz fastq 834710665.0 11441037.0 GSM6068602 r3 0:72.96 1:0 A:225104441;C:191764824;G:196384217;T:220771605;N:685578 72 0     225104441 191764824 196384217 220771605 685578 SRX15004842 SRS12753554 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93233   0.05582   0.76159   0.51481   74   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69591 69591 SRR18927195 SRX15004842 SRS12753554 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1 GSM6068602   source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endothelium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage GSM6068602 GSM6068602: FAC sorted GFP cells 15 s Tgfli1a:egfp rep 1; Danio rerio; RNA Seq GSM6068602 r1 GSM6068602 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     fliegfp_01_S7_L004_R1_001.fastq.gz fastq 851008802.0 11646797.0 GSM6068602 r4 0:73.07 1:0 A:229587437;C:195482220;G:199880005;T:225397616;N:661524 73 0     229587437 195482220 199880005 225397616 661524 SRX15004842 SRS12753554 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.93162   0.05617   0.76195   0.51057   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Endothelium Cardiovascular System
69592 69592 SRR18927196 SRX15004841 SRS12753553 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Gtendocard:egfp rep 3 GSM6068601   source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Gtendocard:egfp rep 3 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endocardium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage GSM6068601 GSM6068601: FAC sorted GFP cells 15 s Gtendocard:egfp rep 3; Danio rerio; RNA Seq GSM6068601 r1 GSM6068601 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     endocardegfp_03_S3_L001_R1_001.fastq.gz fastq 789993899.0 10821883.0 GSM6068601 r1 0:73.00 1:0 A:215890135;C:178235825;G:183043642;T:212180982;N:643315 73 0     215890135 178235825 183043642 212180982 643315 SRX15004841 SRS12753553 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.94291   0.0758   0.75071   0.46413   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Heart Cardiovascular System
69593 69593 SRR18927197 SRX15004841 SRS12753553 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Gtendocard:egfp rep 3 GSM6068601   source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Gtendocard:egfp rep 3 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endocardium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage GSM6068601 GSM6068601: FAC sorted GFP cells 15 s Gtendocard:egfp rep 3; Danio rerio; RNA Seq GSM6068601 r1 GSM6068601 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     endocardegfp_03_S3_L002_R1_001.fastq.gz fastq 761479840.0 10440053.0 GSM6068601 r2 0:72.94 1:0 A:208204230;C:172086666;G:175892087;T:204676185;N:620672 72 0     208204230 172086666 175892087 204676185 620672 SRX15004841 SRS12753553 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.94452   0.07485   0.74998   0.50338   38   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Heart Cardiovascular System
69594 69594 SRR18927198 SRX15004841 SRS12753553 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Gtendocard:egfp rep 3 GSM6068601   source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Gtendocard:egfp rep 3 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endocardium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage GSM6068601 GSM6068601: FAC sorted GFP cells 15 s Gtendocard:egfp rep 3; Danio rerio; RNA Seq GSM6068601 r1 GSM6068601 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     endocardegfp_03_S3_L003_R1_001.fastq.gz fastq 765660473.0 10491638.0 GSM6068601 r3 0:72.98 1:0 A:209572424;C:172800895;G:176915262;T:205772587;N:599305 72 0     209572424 172800895 176915262 205772587 599305 SRX15004841 SRS12753553 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.94355   0.07527   0.75055   0.50343   74   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Heart Cardiovascular System
69595 69595 SRR18927199 SRX15004841 SRS12753553 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Gtendocard:egfp rep 3 GSM6068601   source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Gtendocard:egfp rep 3 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endocardium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage GSM6068601 GSM6068601: FAC sorted GFP cells 15 s Gtendocard:egfp rep 3; Danio rerio; RNA Seq GSM6068601 r1 GSM6068601 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     endocardegfp_03_S3_L004_R1_001.fastq.gz fastq 776554362.0 10626636.0 GSM6068601 r4 0:73.08 1:0 A:212610309;C:175329364;G:179249787;T:208800328;N:564574 73 0     212610309 175329364 179249787 208800328 564574 SRX15004841 SRS12753553 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.94493   0.07566   0.74953   0.50021   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Heart Cardiovascular System
69596 69596 SRR18927200 SRX15004840 SRS12753552 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Gtendocard:egfp rep 2 GSM6068600   source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Gtendocard:egfp rep 2 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endocardium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage GSM6068600 GSM6068600: FAC sorted GFP cells 15 s Gtendocard:egfp rep 2; Danio rerio; RNA Seq GSM6068600 r1 GSM6068600 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     endocardegfp_02_S2_L001_R1_001.fastq.gz fastq 751429636.0 10278996.0 GSM6068600 r1 0:73.10 1:0 A:204301691;C:170664268;G:175292596;T:200617007;N:554074 73 0     204301691 170664268 175292596 200617007 554074 SRX15004840 SRS12753552 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.94194   0.08592   0.74757   0.48366   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Heart Cardiovascular System
69597 69597 SRR18927201 SRX15004840 SRS12753552 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Gtendocard:egfp rep 2 GSM6068600   source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Gtendocard:egfp rep 2 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endocardium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage GSM6068600 GSM6068600: FAC sorted GFP cells 15 s Gtendocard:egfp rep 2; Danio rerio; RNA Seq GSM6068600 r1 GSM6068600 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     endocardegfp_02_S2_L002_R1_001.fastq.gz fastq 719889768.0 9853923.0 GSM6068600 r2 0:73.06 1:0 A:195863070;C:163754101;G:167421766;T:192323572;N:527259 73 0     195863070 163754101 167421766 192323572 527259 SRX15004840 SRS12753552 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.94449   0.08745   0.74541   0.48655   73   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Heart Cardiovascular System
69598 69598 SRR18927202 SRX15004840 SRS12753552 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Gtendocard:egfp rep 2 GSM6068600   source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Gtendocard:egfp rep 2 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endocardium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage GSM6068600 GSM6068600: FAC sorted GFP cells 15 s Gtendocard:egfp rep 2; Danio rerio; RNA Seq GSM6068600 r1 GSM6068600 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     endocardegfp_02_S2_L003_R1_001.fastq.gz fastq 727065663.0 9943220.0 GSM6068600 r3 0:73.12 1:0 A:198000516;C:165197580;G:169210147;T:194173311;N:484109 73 0     198000516 165197580 169210147 194173311 484109 SRX15004840 SRS12753552 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.94266   0.08637   0.74842   0.49201   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Heart Cardiovascular System
69599 69599 SRR18927203 SRX15004840 SRS12753552 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Gtendocard:egfp rep 2 GSM6068600   source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Gtendocard:egfp rep 2 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endocardium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage GSM6068600 GSM6068600: FAC sorted GFP cells 15 s Gtendocard:egfp rep 2; Danio rerio; RNA Seq GSM6068600 r1 GSM6068600 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     endocardegfp_02_S2_L004_R1_001.fastq.gz fastq 741109568.0 10117795.0 GSM6068600 r4 0:73.25 1:0 A:201911109;C:168382932;G:172244312;T:198133836;N:437379 73 0     201911109 168382932 172244312 198133836 437379 SRX15004840 SRS12753552 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.94383   0.0868   0.74775   0.48514   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Heart Cardiovascular System
69600 69600 SRR18927204 SRX15004839 SRS12753551 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Gtendocard:egfp rep 1 GSM6068599   source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Gtendocard:egfp rep 1 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endocardium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage GSM6068599 GSM6068599: FAC sorted GFP cells 15 s Gtendocard:egfp rep 1; Danio rerio; RNA Seq GSM6068599 r1 GSM6068599 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     endocardegfp_01_S1_L001_R1_001.fastq.gz fastq 738191052.0 10120241.0 GSM6068599 r1 0:72.94 1:0 A:201379342;C:167003879;G:171545653;T:197622863;N:639315 72 0     201379342 167003879 171545653 197622863 639315 SRX15004839 SRS12753551 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.94529   0.0782   0.74485   0.47776   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Heart Cardiovascular System
69601 69601 SRR18927205 SRX15004839 SRS12753551 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Gtendocard:egfp rep 1 GSM6068599   source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Gtendocard:egfp rep 1 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endocardium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage GSM6068599 GSM6068599: FAC sorted GFP cells 15 s Gtendocard:egfp rep 1; Danio rerio; RNA Seq GSM6068599 r1 GSM6068599 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     endocardegfp_01_S1_L002_R1_001.fastq.gz fastq 711040088.0 9755308.0 GSM6068599 r2 0:72.89 1:0 A:194155066;C:161121776;G:164711634;T:190419378;N:632234 72 0     194155066 161121776 164711634 190419378 632234 SRX15004839 SRS12753551 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.94633   0.07791   0.74698   0.4735   75   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Heart Cardiovascular System
69602 69602 SRR18927206 SRX15004839 SRS12753551 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Gtendocard:egfp rep 1 GSM6068599   source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Gtendocard:egfp rep 1 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endocardium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage GSM6068599 GSM6068599: FAC sorted GFP cells 15 s Gtendocard:egfp rep 1; Danio rerio; RNA Seq GSM6068599 r1 GSM6068599 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     endocardegfp_01_S1_L003_R1_001.fastq.gz fastq 715401139.0 9809891.0 GSM6068599 r3 0:72.93 1:0 A:195488921;C:161934876;G:165831694;T:191545949;N:599699 72 0     195488921 161934876 165831694 191545949 599699 SRX15004839 SRS12753551 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.94581   0.07803   0.74669   0.47106   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Heart Cardiovascular System
69603 69603 SRR18927207 SRX15004839 SRS12753551 SRP372368 PRJNA832312 Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2 GSE201611 Transcriptome Analysis The endocardium plays important roles in the development and function of the vertebrate heart; however few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity we employed npas4l etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression whereas Bmp inhibition decreased expression. Finally epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together these results describe the differentiation of the endocardium distinct from vasculature and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish three independent biological replicates were collected for each condition   pubmed:35531980   FAC sorted GFP cells 15 s Gtendocard:egfp rep 1 GSM6068599   source name:Endocardium|tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage FAC sorted GFP cells 15 s Gtendocard:egfp rep 1 Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output Endocardium   Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147 Fish were allowed to lay eggs in a 30 minute window fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage tissue:Endocardium|transgenic line:GtSAGFF27C; Tg4xUAS:egfp|genotype:WT|developmental stage:15 somite stage GSM6068599 GSM6068599: FAC sorted GFP cells 15 s Gtendocard:egfp rep 1; Danio rerio; RNA Seq GSM6068599 r1 GSM6068599 1 Embryos were collected deyolked and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries libraries were prepared using the Smart seq2 protocol as described by Picelli et al. 2014 PMID:24385147   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA NextSeq 500   SRP372368     endocardegfp_01_S1_L004_R1_001.fastq.gz fastq 728825483.0 9979191.0 GSM6068599 r4 0:73.03 1:0 A:199202075;C:165019655;G:168738823;T:195306351;N:558579 73 0     199202075 165019655 168738823 195306351 558579 SRX15004839 SRS12753551 SRA1410588 Department of Anatomy & Physiology, The University of Melbourne Department of Anatomy & Physiology, The University of Melbourne 1 0.94656   0.07945   0.7471   0.47584   76   B   usable mapping rate illumina nextseq unknown cdna_unspecified unknown sc single_cell_plate smartseq   Australia 2022-04-26 Segmentation Embryo Heart Cardiovascular System

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