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
49040,SRR7633494,SRX4497225,SRS3618225,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,G2 endo 03,GSM3317066,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA,G2 endo 03,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:human APOL1 G2 mRNA,GSM3317066,GSM3317066: G2 endo 03; Danio rerio; RNA Seq,GSM3317066,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317066,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S18_trimmed.fastq.gz,fastq,950344310.0,18847513.0,GSM3317066 r1,0:50.42 1:0,A:270135652;C:209210468;G:202674675;T:268256430;N:67085,50,0,,,270135652,209210468,202674675,268256430,67085,SRX4497225,SRS3618225,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.89759,,0.1428,,0.69132,,0.4729,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49041,SRR7633493,SRX4497224,SRS3618224,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,G2 endo 02,GSM3317065,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA,G2 endo 02,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:human APOL1 G2 mRNA,GSM3317065,GSM3317065: G2 endo 02; Danio rerio; RNA Seq,GSM3317065,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317065,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S17_trimmed.fastq.gz,fastq,1635110054.0,32380584.0,GSM3317065 r1,0:50.50 1:0,A:462134552;C:361057634;G:349465446;T:462337205;N:115217,50,0,,,462134552,361057634,349465446,462337205,115217,SRX4497224,SRS3618224,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.80201,,0.12711,,0.70471,,0.44427,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49042,SRR7633492,SRX4497223,SRS3618223,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,G2 endo 01,GSM3317064,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G2 mRNA,G2 endo 01,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:human APOL1 G2 mRNA,GSM3317064,GSM3317064: G2 endo 01; Danio rerio; RNA Seq,GSM3317064,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317064,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S16_trimmed.fastq.gz,fastq,1302352614.0,25794210.0,GSM3317064 r1,0:50.49 1:0,A:370194702;C:286011167;G:276758200;T:369297736;N:90809,50,0,,,370194702,286011167,276758200,369297736,90809,SRX4497223,SRS3618223,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.89468,,0.15745,,0.69447,,0.47938,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49043,SRR7633491,SRX4497222,SRS3618222,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,G0 endo 03,GSM3317063,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA,G0 endo 03,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:human APOL1 G0 mRNA,GSM3317063,GSM3317063: G0 endo 03; Danio rerio; RNA Seq,GSM3317063,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317063,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S15_trimmed.fastq.gz,fastq,1248556473.0,24725241.0,GSM3317063 r1,0:50.50 1:0,A:350256976;C:280431139;G:270771772;T:347009294;N:87292,50,0,,,350256976,280431139,270771772,347009294,87292,SRX4497222,SRS3618222,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.90514,,0.13266,,0.69236,,0.47977,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49044,SRR7633490,SRX4497221,SRS3618221,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,G0 endo 02,GSM3317062,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA,G0 endo 02,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:human APOL1 G0 mRNA,GSM3317062,GSM3317062: G0 endo 02; Danio rerio; RNA Seq,GSM3317062,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317062,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S14_trimmed.fastq.gz,fastq,372093672.0,7456111.0,GSM3317062 r1,0:49.90 1:0,A:113486766;C:74400549;G:71245468;T:112935661;N:25228,49,0,,,113486766,74400549,71245468,112935661,25228,SRX4497221,SRS3618221,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.89644,,0.12968,,0.70658,,0.47231,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49045,SRR7633489,SRX4497220,SRS3618220,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,G0 endo 01,GSM3317061,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:human APOL1 G0 mRNA,G0 endo 01,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:human APOL1 G0 mRNA,GSM3317061,GSM3317061: G0 endo 01; Danio rerio; RNA Seq,GSM3317061,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317061,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S13_trimmed.fastq.gz,fastq,1450133780.0,28705598.0,GSM3317061 r1,0:50.52 1:0,A:407543677;C:323333189;G:313321100;T:405835253;N:100561,50,0,,,407543677,323333189,313321100,405835253,100561,SRX4497220,SRS3618220,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.8994,,0.13347,,0.6942,,0.47759,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49046,SRR7633488,SRX4497219,SRS3618219,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,control endo 03,GSM3317060,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:control,control endo 03,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:control,GSM3317060,GSM3317060: control endo 03; Danio rerio; RNA Seq,GSM3317060,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317060,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S12_trimmed.fastq.gz,fastq,1720199608.0,34019943.0,GSM3317060 r1,0:50.56 1:0,A:474252335;C:393152371;G:382256277;T:470417173;N:121452,50,0,,,474252335,393152371,382256277,470417173,121452,SRX4497219,SRS3618219,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.90252,,0.11709,,0.69668,,0.47424,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49047,SRR7633487,SRX4497218,SRS3618218,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,control endo 02,GSM3317059,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:control,control endo 02,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:control,GSM3317059,GSM3317059: control endo 02; Danio rerio; RNA Seq,GSM3317059,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317059,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S11_trimmed.fastq.gz,fastq,322327295.0,6605687.0,GSM3317059 r1,0:48.80 1:0,A:109722776;C:53179948;G:51091267;T:108312123;N:21181,48,0,,,109722776,53179948,51091267,108312123,21181,SRX4497218,SRS3618218,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.8922,,0.1261,,0.72811,,0.46128,,50,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
49048,SRR7633486,SRX4497217,SRS3618217,SRP155992,PRJNA483985,Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA,GSE118000,Transcriptome Analysis,We injected zebrafish embryos with human APOL1 mRNA  dissociated embryos at xxx days of age  and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting  mRNA was extracted from purified cells and used to generate cDNA libraries  which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham  APOL1 G0  APOL1 G2,,pubmed:31158233,,control endo 01,GSM3317058,,tissue:zebrafish endothelium|line:fli:EGFP|treatment:control,control endo 01,Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered  sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2,zebrafish endothelium,Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL  or phenol red,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf,line:fli:EGFP|treatment:control,GSM3317058,GSM3317058: control endo 01; Danio rerio; RNA Seq,GSM3317058,,1,RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech,GEO Accession:GSM3317058,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina HiSeq 2500,,SRP155992,,,BA_S10_trimmed.fastq.gz,fastq,1484074935.0,29385409.0,GSM3317058 r1,0:50.50 1:0,A:411414710;C:336260838;G:326730208;T:409563857;N:105322,50,0,,,411414710,336260838,326730208,409563857,105322,SRX4497217,SRS3618217,SRA749599,GEO,"Duke Molecular Physiology Institute, Duke University Medical Center",1,0.88777,,0.11462,,0.70102,,0.47353,,49,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,United States,2018-08-01,Larval,Larval,Endothelium,Cardiovascular System
69580,SRR18927184,SRX15004844,SRS12753556,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however  few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here  we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity  we employed npas4l  etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants  significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression  whereas Bmp inhibition decreased expression. Finally  epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast  overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together  these results describe the differentiation of the endocardium  distinct from vasculature  and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish  three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 3,GSM6068604,,source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 3,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endothelium,,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window  fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068604,GSM6068604: FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 3; Danio rerio; RNA Seq,GSM6068604 r1,GSM6068604,1,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,fliegfp_03_S9_L001_R1_001.fastq.gz,fastq,744134237.0,10221322.0,GSM6068604 r1,0:72.80 1:0,A:200415459;C:170890467;G:175699158;T:196451943;N:677210,72,0,,,200415459,170890467,175699158,196451943,677210,SRX15004844,SRS12753556,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.93677,,0.0458,,0.76144,,0.51338,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Endothelium,Cardiovascular System
69581,SRR18927185,SRX15004844,SRS12753556,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however  few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here  we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity  we employed npas4l  etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants  significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression  whereas Bmp inhibition decreased expression. Finally  epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast  overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together  these results describe the differentiation of the endocardium  distinct from vasculature  and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish  three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 3,GSM6068604,,source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 3,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endothelium,,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window  fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068604,GSM6068604: FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 3; Danio rerio; RNA Seq,GSM6068604 r1,GSM6068604,1,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,fliegfp_03_S9_L002_R1_001.fastq.gz,fastq,713336563.0,9806369.0,GSM6068604 r2,0:72.74 1:0,A:192232089;C:164110978;G:167926911;T:188411430;N:655155,72,0,,,192232089,164110978,167926911,188411430,655155,SRX15004844,SRS12753556,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.93575,,0.0459,,0.7628,,0.52271,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Endothelium,Cardiovascular System
69582,SRR18927186,SRX15004844,SRS12753556,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however  few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here  we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity  we employed npas4l  etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants  significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression  whereas Bmp inhibition decreased expression. Finally  epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast  overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together  these results describe the differentiation of the endocardium  distinct from vasculature  and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish  three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 3,GSM6068604,,source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 3,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endothelium,,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window  fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068604,GSM6068604: FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 3; Danio rerio; RNA Seq,GSM6068604 r1,GSM6068604,1,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,fliegfp_03_S9_L003_R1_001.fastq.gz,fastq,718617566.0,9871758.0,GSM6068604 r3,0:72.80 1:0,A:193895503;C:165112470;G:169254039;T:189730714;N:624840,72,0,,,193895503,165112470,169254039,189730714,624840,SRX15004844,SRS12753556,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.9355,,0.04598,,0.76459,,0.5158,,73,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Endothelium,Cardiovascular System
69583,SRR18927187,SRX15004844,SRS12753556,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however  few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here  we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity  we employed npas4l  etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants  significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression  whereas Bmp inhibition decreased expression. Finally  epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast  overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together  these results describe the differentiation of the endocardium  distinct from vasculature  and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish  three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 3,GSM6068604,,source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 3,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endothelium,,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window  fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068604,GSM6068604: FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 3; Danio rerio; RNA Seq,GSM6068604 r1,GSM6068604,1,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,fliegfp_03_S9_L004_R1_001.fastq.gz,fastq,727564590.0,9976511.0,GSM6068604 r4,0:72.93 1:0,A:196363760;C:167163486;G:171092104;T:192383180;N:562060,72,0,,,196363760,167163486,171092104,192383180,562060,SRX15004844,SRS12753556,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.93595,,0.04601,,0.76353,,0.51732,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Endothelium,Cardiovascular System
69584,SRR18927188,SRX15004843,SRS12753555,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however  few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here  we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity  we employed npas4l  etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants  significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression  whereas Bmp inhibition decreased expression. Finally  epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast  overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together  these results describe the differentiation of the endocardium  distinct from vasculature  and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish  three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 2,GSM6068603,,source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 2,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endothelium,,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window  fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068603,GSM6068603: FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 2; Danio rerio; RNA Seq,GSM6068603 r1,GSM6068603,1,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,fliegfp_02_S8_L001_R1_001.fastq.gz,fastq,697802741.0,9548738.0,GSM6068603 r1,0:73.08 1:0,A:187922068;C:160061203;G:164649390;T:184626878;N:543202,73,0,,,187922068,160061203,164649390,184626878,543202,SRX15004843,SRS12753555,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.93586,,0.05129,,0.76424,,0.52169,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Endothelium,Cardiovascular System
69585,SRR18927189,SRX15004843,SRS12753555,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however  few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here  we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity  we employed npas4l  etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants  significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression  whereas Bmp inhibition decreased expression. Finally  epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast  overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together  these results describe the differentiation of the endocardium  distinct from vasculature  and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish  three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 2,GSM6068603,,source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 2,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endothelium,,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window  fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068603,GSM6068603: FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 2; Danio rerio; RNA Seq,GSM6068603 r1,GSM6068603,1,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,fliegfp_02_S8_L002_R1_001.fastq.gz,fastq,662903444.0,9078930.0,GSM6068603 r2,0:73.02 1:0,A:178605669;C:152357709;G:156008633;T:175409889;N:521544,73,0,,,178605669,152357709,156008633,175409889,521544,SRX15004843,SRS12753555,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.93653,,0.05146,,0.7628,,0.51778,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Endothelium,Cardiovascular System
69586,SRR18927190,SRX15004843,SRS12753555,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however  few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here  we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity  we employed npas4l  etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants  significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression  whereas Bmp inhibition decreased expression. Finally  epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast  overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together  these results describe the differentiation of the endocardium  distinct from vasculature  and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish  three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 2,GSM6068603,,source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 2,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endothelium,,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window  fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068603,GSM6068603: FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 2; Danio rerio; RNA Seq,GSM6068603 r1,GSM6068603,1,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,fliegfp_02_S8_L003_R1_001.fastq.gz,fastq,668311097.0,9143688.0,GSM6068603 r3,0:73.09 1:0,A:180289485;C:153373494;G:157331239;T:176839110;N:477769,73,0,,,180289485,153373494,157331239,176839110,477769,SRX15004843,SRS12753555,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.93696,,0.05225,,0.7637,,0.51732,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Endothelium,Cardiovascular System
69587,SRR18927191,SRX15004843,SRS12753555,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however  few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here  we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity  we employed npas4l  etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants  significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression  whereas Bmp inhibition decreased expression. Finally  epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast  overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together  these results describe the differentiation of the endocardium  distinct from vasculature  and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish  three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 2,GSM6068603,,source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 2,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endothelium,,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window  fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068603,GSM6068603: FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 2; Danio rerio; RNA Seq,GSM6068603 r1,GSM6068603,1,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,fliegfp_02_S8_L004_R1_001.fastq.gz,fastq,680968806.0,9296775.0,GSM6068603 r4,0:73.25 1:0,A:183838465;C:156195225;G:160056448;T:180449193;N:429475,73,0,,,183838465,156195225,160056448,180449193,429475,SRX15004843,SRS12753555,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.93695,,0.05036,,0.76394,,0.52148,,55,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Endothelium,Cardiovascular System
69588,SRR18927192,SRX15004842,SRS12753554,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however  few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here  we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity  we employed npas4l  etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants  significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression  whereas Bmp inhibition decreased expression. Finally  epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast  overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together  these results describe the differentiation of the endocardium  distinct from vasculature  and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish  three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 1,GSM6068602,,source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 1,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endothelium,,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window  fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068602,GSM6068602: FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 1; Danio rerio; RNA Seq,GSM6068602 r1,GSM6068602,1,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,fliegfp_01_S7_L001_R1_001.fastq.gz,fastq,860623909.0,11793192.0,GSM6068602 r1,0:72.98 1:0,A:231785480;C:197544026;G:202920509;T:227621795;N:752099,72,0,,,231785480,197544026,202920509,227621795,752099,SRX15004842,SRS12753554,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.93103,,0.0562,,0.76179,,0.51243,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Endothelium,Cardiovascular System
69589,SRR18927193,SRX15004842,SRS12753554,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however  few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here  we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity  we employed npas4l  etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants  significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression  whereas Bmp inhibition decreased expression. Finally  epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast  overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together  these results describe the differentiation of the endocardium  distinct from vasculature  and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish  three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 1,GSM6068602,,source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 1,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endothelium,,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window  fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068602,GSM6068602: FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 1; Danio rerio; RNA Seq,GSM6068602 r1,GSM6068602,1,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,fliegfp_01_S7_L002_R1_001.fastq.gz,fastq,829335984.0,11372967.0,GSM6068602 r2,0:72.92 1:0,A:223480519;C:190755977;G:194990382;T:219387236;N:721870,72,0,,,223480519,190755977,194990382,219387236,721870,SRX15004842,SRS12753554,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.93059,,0.05558,,0.76106,,0.51174,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Endothelium,Cardiovascular System
69590,SRR18927194,SRX15004842,SRS12753554,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however  few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here  we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity  we employed npas4l  etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants  significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression  whereas Bmp inhibition decreased expression. Finally  epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast  overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together  these results describe the differentiation of the endocardium  distinct from vasculature  and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish  three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 1,GSM6068602,,source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 1,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endothelium,,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window  fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068602,GSM6068602: FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 1; Danio rerio; RNA Seq,GSM6068602 r1,GSM6068602,1,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,fliegfp_01_S7_L003_R1_001.fastq.gz,fastq,834710665.0,11441037.0,GSM6068602 r3,0:72.96 1:0,A:225104441;C:191764824;G:196384217;T:220771605;N:685578,72,0,,,225104441,191764824,196384217,220771605,685578,SRX15004842,SRS12753554,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.93233,,0.05582,,0.76159,,0.51481,,74,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Endothelium,Cardiovascular System
69591,SRR18927195,SRX15004842,SRS12753554,SRP372368,PRJNA832312,Endocardial identity is established during early somitogenesis by Bmp signalling acting upstream of npas4l and etv2,GSE201611,Transcriptome Analysis,The endocardium plays important roles in the development and function of the vertebrate heart; however  few molecular markers of this tissue have been identified and little is known about what regulates its differentiation. Here  we describe the GtSAGFF27C; Tg4xUAS:egfp line as a marker of endocardial development in zebrafish. Transcriptomic comparison between endocardium and pan endothelium confirms molecular distinction between these populations and time course analysis suggests differentiation as early as eight somites. To investigate what regulates endocardial identity  we employed npas4l  etv2 and scl loss of function models. Endocardial expression is lost in npas4l mutants  significantly reduced in etv2 mutants and only modestly affected upon scl loss of function. Bmp signalling was also examined: overactivation of Bmp signalling increased endocardial expression  whereas Bmp inhibition decreased expression. Finally  epistasis experiments showed that overactivation of Bmp signalling was incapable of restoring endocardial expression in etv2 mutants. By contrast  overexpression of either npas4l or etv2 was sufficient to rescue endocardial expression upon Bmp inhibition. Together  these results describe the differentiation of the endocardium  distinct from vasculature  and place npas4l and etv2 downstream of Bmp signalling in regulating its differentiation. Overall design: Differential gene expression analysis of RNA seq data from GFP positive endocardial GtSAGFF27C; Tg4xUAS:egfp and endothelial Tgfli1a:egfp cells at the 15 somite stage in zebrafish  three independent biological replicates were collected for each condition,,pubmed:35531980,,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 1,GSM6068602,,source name:Endothelium|tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 1,Trimmed sequence reads were mapped to GRCz11 and counted using the Rsubread package in R Library normalisation and differential expression analysis was performed using the limma package in R Assembly: GRCz11 Supplementary files format and content: Differential expression analysis of endocard:egfp vs fli1a:egfp as a csv file of log2 fold changes and associated statistics from limma output,Endothelium,,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,Fish were allowed to lay eggs in a 30 minute window  fertilised embryos were sorted and grown at a density of 50 per/petri dish in E2 media at 23℃ overnight then allowed to grow at 28.5℃ until they reached the 15 somite stage,tissue:Endothelium|transgenic line:Tgfli1a:egfp|genotype:WT|developmental stage:15 somite stage,GSM6068602,GSM6068602: FAC sorted GFP cells  15 s Tgfli1a:egfp  rep 1; Danio rerio; RNA Seq,GSM6068602 r1,GSM6068602,1,Embryos were collected  deyolked  and dissociated at the 15 somite stage. GFP positive cells were FAC sorted directly into trizol and total RNA extracted using a Direct zol RNA MiniPrep kit Zymo research 2 ng of total RNA from each sample was used for the construction of sequencing libraries  libraries were prepared using the Smart seq2 protocol as described by Picelli et al.  2014 PMID:24385147,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 500,,SRP372368,,,fliegfp_01_S7_L004_R1_001.fastq.gz,fastq,851008802.0,11646797.0,GSM6068602 r4,0:73.07 1:0,A:229587437;C:195482220;G:199880005;T:225397616;N:661524,73,0,,,229587437,195482220,199880005,225397616,661524,SRX15004842,SRS12753554,SRA1410588,"Department of Anatomy & Physiology, The University of Melbourne","Department of Anatomy & Physiology, The University of Melbourne",1,0.93162,,0.05617,,0.76195,,0.51057,,75,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_plate,smartseq,,Australia,2022-04-26,Segmentation,Embryo,Endothelium,Cardiovascular System