rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
25170,SRR25661605,SRX21387413,SRS18627977,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD+/? 20 hpf CMs rep3,GSM7714404,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD+/? 20 hpf CMs rep3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS,GSM7714404,GSM7714404: hand2 FLD+/? 20 hpf CMs rep3; Danio rerio; RNA Seq,GSM7714404 r1,GSM7714404,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_het_3_R1.fastq.gz,fastq,2441736984.0,34141777.0,GSM7714404 r1,0:71.52,A:706186414;C:496261994;G:526176364;T:713112212;N:0,71,,,,706186414,496261994,526176364,713112212,0,SRX21387413,SRS18627977,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.9026,,0.15816,,0.76278,,0.44042,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25171,SRR25661606,SRX21387412,SRS18627976,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD+/? 20 hpf CMs rep2,GSM7714403,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD+/? 20 hpf CMs rep2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS,GSM7714403,GSM7714403: hand2 FLD+/? 20 hpf CMs rep2; Danio rerio; RNA Seq,GSM7714403 r1,GSM7714403,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_het_2_R1.fastq.gz,fastq,2185611269.0,30558084.0,GSM7714403 r1,0:71.52,A:612617675;C:458632518;G:474458738;T:639902338;N:0,71,,,,612617675,458632518,474458738,639902338,0,SRX21387412,SRS18627976,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90042,,0.14005,,0.75424,,0.44277,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25172,SRR25661607,SRX21387411,SRS18627975,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD+/? 20 hpf CMs rep1,GSM7714402,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD+/? 20 hpf CMs rep1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 mutants|treatment:sorted cells by FACS,GSM7714402,GSM7714402: hand2 FLD+/? 20 hpf CMs rep1; Danio rerio; RNA Seq,GSM7714402 r1,GSM7714402,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_het_1_R1.fastq.gz,fastq,2291884894.0,32043147.0,GSM7714402 r1,0:71.52,A:635094975;C:489594953;G:499909828;T:667285138;N:0,71,,,,635094975,489594953,499909828,667285138,0,SRX21387411,SRS18627975,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90883,,0.14288,,0.75331,,0.44459,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25173,SRR25661608,SRX21387410,SRS18627974,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,WT 20 hpf CMs rep3,GSM7714401,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,WT 20 hpf CMs rep3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS,GSM7714401,GSM7714401: WT 20 hpf CMs rep3; Danio rerio; RNA Seq,GSM7714401 r1,GSM7714401,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_CMs_3_R1.fastq.gz,fastq,2268251602.0,31717610.0,GSM7714401 r1,0:71.51,A:637196241;C:477782543;G:497683941;T:655588877;N:0,71,,,,637196241,477782543,497683941,655588877,0,SRX21387410,SRS18627974,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90026,,0.13291,,0.78707,,0.40811,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25174,SRR25661609,SRX21387409,SRS18627973,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,WT 20 hpf CMs rep2,GSM7714400,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,WT 20 hpf CMs rep2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS,GSM7714400,GSM7714400: WT 20 hpf CMs rep2; Danio rerio; RNA Seq,GSM7714400 r1,GSM7714400,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_CMs_2_R1.fastq.gz,fastq,2195524610.0,30700033.0,GSM7714400 r1,0:71.52,A:615401741;C:462686936;G:481135567;T:636300366;N:0,71,,,,615401741,462686936,481135567,636300366,0,SRX21387409,SRS18627973,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90323,,0.1476,,0.78744,,0.41728,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25175,SRR25661610,SRX21387408,SRS18627972,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,WT 20 hpf CMs rep1,GSM7714399,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,WT 20 hpf CMs rep1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:sibling WT of hand2 OE|treatment:sorted cells by FACS,GSM7714399,GSM7714399: WT 20 hpf CMs rep1; Danio rerio; RNA Seq,GSM7714399 r1,GSM7714399,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_WT_CMs_1_R1.fastq.gz,fastq,2258160684.0,31576661.0,GSM7714399 r1,0:71.51,A:641254288;C:471580136;G:491501482;T:653824778;N:0,71,,,,641254288,471580136,491501482,653824778,0,SRX21387408,SRS18627972,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.9,,0.13993,,0.78445,,0.40575,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25176,SRR25661611,SRX21387407,SRS18627971,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 OE 20 hpf CMs rep3,GSM7714398,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 OE 20 hpf CMs rep3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS,GSM7714398,GSM7714398: hand2 OE 20 hpf CMs rep3; Danio rerio; RNA Seq,GSM7714398 r1,GSM7714398,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_OE_CMs_3_R1.fastq.gz,fastq,1886569909.0,26380170.0,GSM7714398 r1,0:71.51,A:534874421;C:392168718;G:411533838;T:547992932;N:0,71,,,,534874421,392168718,411533838,547992932,0,SRX21387407,SRS18627971,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.89968,,0.14763,,0.77881,,0.42601,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25177,SRR25661612,SRX21387406,SRS18627970,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 OE 20 hpf CMs rep2,GSM7714397,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 OE 20 hpf CMs rep2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS,GSM7714397,GSM7714397: hand2 OE 20 hpf CMs rep2; Danio rerio; RNA Seq,GSM7714397 r1,GSM7714397,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_OE_CMs_2_R1.fastq.gz,fastq,2197151812.0,30722639.0,GSM7714397 r1,0:71.52,A:617116635;C:461951919;G:481371246;T:636712012;N:0,71,,,,617116635,461951919,481371246,636712012,0,SRX21387406,SRS18627970,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90877,,0.14744,,0.77191,,0.42845,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25178,SRR25661613,SRX21387405,SRS18627969,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 OE 20 hpf CMs rep1,GSM7714396,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 OE 20 hpf CMs rep1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:overexpression hand2 in myocardium|treatment:sorted cells by FACS,GSM7714396,GSM7714396: hand2 OE 20 hpf CMs rep1; Danio rerio; RNA Seq,GSM7714396 r1,GSM7714396,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_OE_CMs_1_R1.fastq.gz,fastq,1773398936.0,24797998.0,GSM7714396 r1,0:71.51,A:495618212;C:375438077;G:390377060;T:511965587;N:0,71,,,,495618212,375438077,390377060,511965587,0,SRX21387405,SRS18627969,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.90769,,0.1387,,0.7768,,0.42096,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25179,SRR25661614,SRX21387404,SRS18627968,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD /  20 hpf CMs rep3,GSM7714395,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD /  20 hpf CMs rep3,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS,GSM7714395,GSM7714395: hand2 FLD /  20 hpf CMs rep3; Danio rerio; RNA Seq,GSM7714395 r1,GSM7714395,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_Mut_3_R1.fastq.gz,fastq,2179400259.0,30471965.0,GSM7714395 r1,0:71.52,A:600555691;C:468535203;G:483122661;T:627186704;N:0,71,,,,600555691,468535203,483122661,627186704,0,SRX21387404,SRS18627968,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.91581,,0.12256,,0.75209,,0.43413,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25180,SRR25661615,SRX21387403,SRS18627967,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD /  20 hpf CMs rep2,GSM7714394,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD /  20 hpf CMs rep2,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS,GSM7714394,GSM7714394: hand2 FLD /  20 hpf CMs rep2; Danio rerio; RNA Seq,GSM7714394 r1,GSM7714394,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_Mut_2_R1.fastq.gz,fastq,2340991168.0,32733068.0,GSM7714394 r1,0:71.52,A:647423337;C:500120073;G:514803152;T:678644606;N:0,71,,,,647423337,500120073,514803152,678644606,0,SRX21387403,SRS18627967,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.91231,,0.12561,,0.75118,,0.44445,,71,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
25181,SRR25661616,SRX21387402,SRS18627966,SRP455520,PRJNA1006302,The transcriptome of hand2 loss  and gain of function embryonic cardiomyocytes,GSE241049,Transcriptome Analysis,To gain mechanistic insight into how Hand2 regulates cardiac fusion  we performed transcriptomic analyses of  hand2 loss  and gain of function 20 hpf cardiomyocytes. Overall design: 1. hand2 loss of function: hand2 mutant CMs vs WT sibling CMs  each group has 3 replicates. 2. hand2 gain of function: hand2 OE CMs vs WT sibling CMs  each group has 3 replicates.,,pubmed:39658721,,hand2 FLD /  20 hpf CMs rep1,GSM7714393,,source name:embryonic heart|tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS|geo loc name:missing|collection date:missing,hand2 FLD /  20 hpf CMs rep1,Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 ensemble release 104 using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 log2 ± 0.59  a maximum Benjamini–Hochberg corrected p value of 0.05  and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed. Assembly: danRer11 Supplementary files format and content: library size normalized counts,embryonic heart,,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,tissue:embryonic heart|cell type:cardiomyocytes|genotype:hand2 mutant|treatment:sorted cells by FACS,GSM7714393,GSM7714393: hand2 FLD /  20 hpf CMs rep1; Danio rerio; RNA Seq,GSM7714393 r1,GSM7714393,1,miRNeasy micro Kit Qiagen  using low input DNase protocol Approximately 1ng of total RNA was used as starting material for SMART® Seq HT Kit Takara Bio.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 2000,,SRP455520,,loader:fastq load.py,E22_3458_Yanli_HT_Lib_Mut_1_R1.fastq.gz,fastq,2727863036.0,38140997.0,GSM7714393 r1,0:71.52,A:760867462;C:577539041;G:596986102;T:792470431;N:0,71,,,,760867462,577539041,596986102,792470431,0,SRX21387402,SRS18627966,SRA1694205,MPI for heart and lung research,MPI for heart and lung research,1,0.91175,,0.1342,,0.75282,,0.44063,,72,,B,,usable mapping rate,illumina,nextseq_v2,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2023-08-17,Segmentation,Embryo,Heart,Cardiovascular System
48416,SRR7252518,SRX4157244,SRS3369695,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group3 Library3,GSM3172818,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group3 Library3,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172818,GSM3172818: Group3 Library3; Danio rerio; RNA Seq,GSM3172818,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172818,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group3_Library3_R1.fastq Group3_Library3_R2.fastq,fastq fastq,10582682434.0,52389517.0,GSM3172818 r1,0:101 1:101,A:2920935491;C:2280838256;G:2373423629;T:3004636928;N:2848130,101,101,,,2920935491,2280838256,2373423629,3004636928,2848130,SRX4157244,SRS3369695,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.82243,0.81602,0.34973,0.34907,0.7959,0.80415,0.58533,0.57989,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48417,SRR7252517,SRX4157243,SRS3369694,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group3 Library2,GSM3172817,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group3 Library2,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172817,GSM3172817: Group3 Library2; Danio rerio; RNA Seq,GSM3172817,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172817,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group3_Library2_R2.fastq Group3_Library2_R1.fastq,fastq fastq,8398868312.0,41578556.0,GSM3172817 r1,0:101 1:101,A:2365832903;C:1714320588;G:1799780549;T:2459288921;N:59645351,101,101,,,2365832903,1714320588,1799780549,2459288921,59645351,SRX4157243,SRS3369694,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.80215,0.80055,0.29918,0.29795,0.78139,0.78567,0.53014,0.5304,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48418,SRR7252516,SRX4157242,SRS3369693,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group3 Library1,GSM3172816,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group3 Library1,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172816,GSM3172816: Group3 Library1; Danio rerio; RNA Seq,GSM3172816,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172816,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group3_Library1_R2.fastq Group3_Library1_R1.fastq,fastq fastq,8784708916.0,43488658.0,GSM3172816 r1,0:101 1:101,A:2237850943;C:1944771284;G:2092315228;T:2411084639;N:98686822,101,101,,,2237850943,1944771284,2092315228,2411084639,98686822,SRX4157242,SRS3369693,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.83019,0.80927,0.27745,0.27973,0.78835,0.80835,0.63272,0.63323,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48419,SRR7252515,SRX4157241,SRS3369740,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group2 Library3,GSM3172815,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group2 Library3,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172815,GSM3172815: Group2 Library3; Danio rerio; RNA Seq,GSM3172815,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172815,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group2_Library3_R1.fastq Group2_Library3_R2.fastq,fastq fastq,7224792398.0,35766299.0,GSM3172815 r1,0:101 1:101,A:1966971879;C:1598533948;G:1648392712;T:2008955757;N:1938102,101,101,,,1966971879,1598533948,1648392712,2008955757,1938102,SRX4157241,SRS3369740,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.83962,0.8342,0.30832,0.30786,0.76455,0.77315,0.60778,0.60922,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48420,SRR7252514,SRX4157240,SRS3369692,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group2 Library2,GSM3172814,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group2 Library2,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172814,GSM3172814: Group2 Library2; Danio rerio; RNA Seq,GSM3172814,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172814,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group2_Library2_R1.fastq Group2_Library2_R2.fastq,fastq fastq,7203903174.0,35662887.0,GSM3172814 r1,0:101 1:101,A:2001767256;C:1497645415;G:1580912101;T:2072372149;N:51206253,101,101,,,2001767256,1497645415,1580912101,2072372149,51206253,SRX4157240,SRS3369692,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.77898,0.77807,0.34363,0.34395,0.79034,0.79375,0.5816,0.58087,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48421,SRR7252513,SRX4157239,SRS3369691,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group2 Library1,GSM3172813,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group2 Library1,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172813,GSM3172813: Group2 Library1; Danio rerio; RNA Seq,GSM3172813,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172813,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group2_Library1_R1.fastq Group2_Library1_R2.fastq,fastq fastq,8442759478.0,41795839.0,GSM3172813 r1,0:101 1:101,A:2196493743;C:1822028333;G:1974061919;T:2376981823;N:73193660,101,101,,,2196493743,1822028333,1974061919,2376981823,73193660,SRX4157239,SRS3369691,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.82021,0.79025,0.30166,0.29983,0.79482,0.81481,0.63103,0.63063,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48422,SRR7252512,SRX4157238,SRS3369690,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group1 Library3,GSM3172812,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group1 Library3,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172812,GSM3172812: Group1 Library3; Danio rerio; RNA Seq,GSM3172812,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172812,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group1_Library3_R1.fastq Group1_Library3_R2.fastq,fastq fastq,8304010526.0,41108963.0,GSM3172812 r1,0:101 1:101,A:2312592520;C:1775301647;G:1843137604;T:2370733357;N:2245398,101,101,,,2312592520,1775301647,1843137604,2370733357,2245398,SRX4157238,SRS3369690,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.79607,0.78867,0.28146,0.28007,0.8047,0.81432,0.58876,0.58873,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48423,SRR7252511,SRX4157237,SRS3369689,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group1 Library2,GSM3172811,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group1 Library2,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172811,GSM3172811: Group1 Library2; Danio rerio; RNA Seq,GSM3172811,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172811,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group1_Library2_R1.fastq Group1_Library2_R2.fastq,fastq fastq,8404855794.0,41608197.0,GSM3172811 r1,0:101 1:101,A:2332624405;C:1762786007;G:1853386011;T:2396361483;N:59697888,101,101,,,2332624405,1762786007,1853386011,2396361483,59697888,SRX4157237,SRS3369689,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.80769,0.78126,0.31373,0.30654,0.7781,0.78644,0.53559,0.54605,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
48424,SRR7252510,SRX4157236,SRS3369688,SRP149660,PRJNA474426,RNA Seq of FACS sorted cardiomyocytes,GSE115263,Transcriptome Analysis,The goal of this experiment was to evaluate the expression profile of cardiomyocytes freshly isolated from zebrafish embryos. Here we report mRNA abundance measurements for zebrafish cardiomyocytes at 20 hpf. We found that cardiomyocytes isolated from zebrafish embyros are enriched for orthologues of genes abundant in mammalian iPS derived cardiomyocytes and other in vitro models of cardiomyocytes. It was also enriched with genes required for cardiac development in zebrafish and mammalian models.  Using a rapid throughput CRISPR Cas9 based G0 screening pipeline  we tested 50 abundant transcription factors derived from this profile  rediscoved transcription factors known to be required for cardiac development  and found a novel role for zbtb16a in cardiac development. Overall design: Abundance measurements of cardiomyocytes purified from 20 hpf zebrafish embryos,,pubmed:29974860,,Group1 Library1,GSM3172810,,source name:Cardiomyocytes|tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,Group1 Library1,Reads were filtered with sickle and scythe QC packages Aligned to GRCz10.80 using Tophat2 Abundance estimated with Cufflinks Genome build: GRCz10 Supplementary files format and content: tab delimited text file includes FPKM values for each sample,Cardiomyocytes,Embryos were dissociated and FACS sorted for GFP,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,Embryos were raised in egg water,tissue:cardiomyocytes|developmental stage:20 hpf|strain:Tgmyl7:lifeact GFP|genotype:wild type,GSM3172810,GSM3172810: Group1 Library1; Danio rerio; RNA Seq,GSM3172810,,1,RNA extracted from FACS sorted cells NuGen Ovation V2 RNA Seq cDNA amplification and Ultralow Library DR library prep,GEO Accession:GSM3172810,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP149660,,,Group1_Library1_R1.fastq Group1_Library1_R2.fastq,fastq fastq,8075069988.0,39975594.0,GSM3172810 r1,0:101 1:101,A:2111117991;C:1746554669;G:1884216047;T:2242387738;N:90793543,101,101,,,2111117991,1746554669,1884216047,2242387738,90793543,SRX4157236,SRS3369688,SRA714694,GEO,"Brian Black Lab, CVRI, UCSF",2,0.80138,0.79326,0.29563,0.30562,0.80304,0.81854,0.5754,0.61905,101,101,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2018-06-04,Segmentation,Embryo,Heart,Cardiovascular System
63406,SRR13777260,SRX10162830,SRS8314486,SRP307942,PRJNA704625,RNA sequencing analysis of ZsYellow negative cells and ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes purified from the same 14 16 somites stage Tgnkx2.5:ZsYellow zebrafish embryos,GSE167416,Transcriptome Analysis,The identification of novel cardiomyocyte intrinsic factors that support ventricular function will expand the number of candidate genes and therapeutic options for heart failure  a leading cause of death worldwide. Here  we demonstrate that a conserved RNA binding protein RBPMS2 is required for ventricular function in zebrafish and for myofibril organization and the regulation of intracellular calcium dynamics in zebrafish and human cardiomyocytes. A differential expression screen uncovered co expression of rbpms2a and rbpms2b in zebrafish cardiomyocytes. Double knockout embryos suffer from compromised ventricular filling during the relaxation phase of the cardiac cycle  which significantly reduces cardiac output. Evaluating rbpms2 null embryos with splicing sensitive differential expression analysis  quantitative PCR  and in situ hybridization revealed differential alternative splicing of cardiomyopathy genes including myosin binding protein C3 mybpc3 and phospholamban pln. Cardiomyocytes in double mutant ventricles and those derived from RBPMS2 null human induced pluripotent stem cells exhibit myofibril disarray and calcium handling abnormalities. Taken together  our data suggest that RBPMS2 performs a conserved role in regulating alternative splicing in cardiomyocytes  which is required for sarcomere organization  optimal calcium handling  and cardiac function. Overall design: Tgnkx2.5:ZsYellow zebrafish embryos at the 14 16 somites stage were dissociated to single cells and their ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes were purified by fluorescence activated cell sorting. ZsYellow negative cells from the same embryos were collected in parallel. RNA sequencing analysis was performed on both populations two replicates each and differentially expressed genes were identified.,,pubmed:36367103,,ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes   replicate 2,GSM5104955,,source name:14 16 somites stage Tgnkx2.5:ZsYellow zebrafish embryos|strain:laboratory strain|tissue:ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes|age:14 16 somites stage|genotype:Tgnkx2.5:ZsYellow,ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes   replicate 2,Illumina Offline BaseCaller1.9.3 software used for basecalling. Quality control: Reads were aligned against Zv9/danRer7 using bwa mem v. 0.7.12 r1039 with flags –t 16 –f and mapping rates  fraction of multiply mapping reads  number of unique 20 mers at the 5’ end of the reads  insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.64 In addition  each resulting bam file was randomly down sampled to a million reads  which were aligned against Zv9/danRer7 and read density across genomic features were estimated for RNA Seq specific quality control metrics. Read mapping and quantification: Salmon v. 1.2.1  was used with the following flags:   quant   l IU     validateMappings in paired end mode against the GRCz11/danRer11 genome assembly and ENSEMBL 100 annotation  using all GRCz11 sequences as decoys. Quantification files were processed in R using the TxImport function and per gene counts and TPM estimates were retrieved. Genome build: Zv11/danRer11 Supplementary files format and content: Matrix table with counts and log2 TPM values for every gene and every sample,14 16 somites stage Tgnkx2.5:ZsYellow zebrafish embryos,,Trizol lysis  chloroform extraction and column based purification Qiagen RNeasy Kit. RNA sample quality was evaluated using a 2100 Bioanalyzer Instrument Agilent Technologies. Approximately 50ng of RNA per sample were used to prepare sequencing libraries with the Clontech low input RNA library preparation kit. Libraries were sequenced as paired end 2x50nt on an Illumina HiSeq2500 instrument. polyA based RT priming followed by tagmentation based RNA Seq protcol,,strain:laboratory strain|tissue:ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes|age:14 16 somites stage|genotype:Tgnkx2.5:ZsYellow,GSM5104955,GSM5104955: ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes   replicate 2; Danio rerio; RNA Seq,GSM5104955,,1,Trizol lysis  chloroform extraction and column based purification Qiagen RNeasy Kit. RNA sample quality was evaluated using a 2100 Bioanalyzer Instrument Agilent Technologies. Approximately 50ng of RNA per sample were used to prepare sequencing libraries with the Clontech low input RNA library preparation kit. Libraries were sequenced as paired end 2x50nt on an Illumina HiSeq2500 instrument. polyA based RT priming followed by tagmentation based RNA Seq protcol,GEO Accession:GSM5104955,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP307942,,,130107Bur_D13-183_1_sequence.fastq.gz 130107Bur_D13-183_2_sequence.fastq.gz,fastq fastq,4545216160.0,56815202.0,GSM5104955 r1,0:40 1:40,A:1317905013;C:913569716;G:959980240;T:1351063436;N:2697755,40,40,,,1317905013,913569716,959980240,1351063436,2697755,SRX10162830,SRS8314486,SRA1199702,GEO,"BioMicro Center / IGE, Biology / Koch Institute / Bioengineering / CEHS, Massachusetts Institute of Technology",2,0.93062,0.75104,0.14171,0.10526,0.74223,0.76134,0.49218,0.4928,40,40,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-02-24,Segmentation,Embryo,Heart,Cardiovascular System
63407,SRR13777259,SRX10162829,SRS8314485,SRP307942,PRJNA704625,RNA sequencing analysis of ZsYellow negative cells and ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes purified from the same 14 16 somites stage Tgnkx2.5:ZsYellow zebrafish embryos,GSE167416,Transcriptome Analysis,The identification of novel cardiomyocyte intrinsic factors that support ventricular function will expand the number of candidate genes and therapeutic options for heart failure  a leading cause of death worldwide. Here  we demonstrate that a conserved RNA binding protein RBPMS2 is required for ventricular function in zebrafish and for myofibril organization and the regulation of intracellular calcium dynamics in zebrafish and human cardiomyocytes. A differential expression screen uncovered co expression of rbpms2a and rbpms2b in zebrafish cardiomyocytes. Double knockout embryos suffer from compromised ventricular filling during the relaxation phase of the cardiac cycle  which significantly reduces cardiac output. Evaluating rbpms2 null embryos with splicing sensitive differential expression analysis  quantitative PCR  and in situ hybridization revealed differential alternative splicing of cardiomyopathy genes including myosin binding protein C3 mybpc3 and phospholamban pln. Cardiomyocytes in double mutant ventricles and those derived from RBPMS2 null human induced pluripotent stem cells exhibit myofibril disarray and calcium handling abnormalities. Taken together  our data suggest that RBPMS2 performs a conserved role in regulating alternative splicing in cardiomyocytes  which is required for sarcomere organization  optimal calcium handling  and cardiac function. Overall design: Tgnkx2.5:ZsYellow zebrafish embryos at the 14 16 somites stage were dissociated to single cells and their ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes were purified by fluorescence activated cell sorting. ZsYellow negative cells from the same embryos were collected in parallel. RNA sequencing analysis was performed on both populations two replicates each and differentially expressed genes were identified.,,pubmed:36367103,,ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes   replicate 1,GSM5104954,,source name:14 16 somites stage Tgnkx2.5:ZsYellow zebrafish embryos|strain:laboratory strain|tissue:ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes|age:14 16 somites stage|genotype:Tgnkx2.5:ZsYellow,ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes   replicate 1,Illumina Offline BaseCaller1.9.3 software used for basecalling. Quality control: Reads were aligned against Zv9/danRer7 using bwa mem v. 0.7.12 r1039 with flags –t 16 –f and mapping rates  fraction of multiply mapping reads  number of unique 20 mers at the 5’ end of the reads  insert size distributions and fraction of ribosomal RNAs were calculated using dedicated perl scripts and bedtools v. 2.25.0.64 In addition  each resulting bam file was randomly down sampled to a million reads  which were aligned against Zv9/danRer7 and read density across genomic features were estimated for RNA Seq specific quality control metrics. Read mapping and quantification: Salmon v. 1.2.1  was used with the following flags:   quant   l IU     validateMappings in paired end mode against the GRCz11/danRer11 genome assembly and ENSEMBL 100 annotation  using all GRCz11 sequences as decoys. Quantification files were processed in R using the TxImport function and per gene counts and TPM estimates were retrieved. Genome build: Zv11/danRer11 Supplementary files format and content: Matrix table with counts and log2 TPM values for every gene and every sample,14 16 somites stage Tgnkx2.5:ZsYellow zebrafish embryos,,Trizol lysis  chloroform extraction and column based purification Qiagen RNeasy Kit. RNA sample quality was evaluated using a 2100 Bioanalyzer Instrument Agilent Technologies. Approximately 50ng of RNA per sample were used to prepare sequencing libraries with the Clontech low input RNA library preparation kit. Libraries were sequenced as paired end 2x50nt on an Illumina HiSeq2500 instrument. polyA based RT priming followed by tagmentation based RNA Seq protcol,,strain:laboratory strain|tissue:ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes|age:14 16 somites stage|genotype:Tgnkx2.5:ZsYellow,GSM5104954,GSM5104954: ZsYellow positive cardiopharyngeal progenitors and cardiomyocytes   replicate 1; Danio rerio; RNA Seq,GSM5104954,,1,Trizol lysis  chloroform extraction and column based purification Qiagen RNeasy Kit. RNA sample quality was evaluated using a 2100 Bioanalyzer Instrument Agilent Technologies. Approximately 50ng of RNA per sample were used to prepare sequencing libraries with the Clontech low input RNA library preparation kit. Libraries were sequenced as paired end 2x50nt on an Illumina HiSeq2500 instrument. polyA based RT priming followed by tagmentation based RNA Seq protcol,GEO Accession:GSM5104954,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 2000,,SRP307942,,,130107Bur_D13-182_1_sequence.fastq.gz 130107Bur_D13-182_2_sequence.fastq.gz,fastq fastq,3727548800.0,46594360.0,GSM5104954 r1,0:40 1:40,A:1076485047;C:747480315;G:792531345;T:1108844452;N:2207641,40,40,,,1076485047,747480315,792531345,1108844452,2207641,SRX10162829,SRS8314485,SRA1199702,GEO,"BioMicro Center / IGE, Biology / Koch Institute / Bioengineering / CEHS, Massachusetts Institute of Technology",2,0.92186,0.71124,0.15892,0.11111,0.74018,0.7625,0.49055,0.48153,40,40,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2021-02-24,Segmentation,Embryo,Heart,Cardiovascular System
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
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,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,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,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,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,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,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,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,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,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,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,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