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
29145,SRR32025076,SRX27375413,SRS23810876,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,qKO 5  biol rep 1  adult aorta  3 aortas pooled,GSM8741276,,source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing,qKO 5  biol rep 1  adult aorta  3 aortas pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 adult aortas and bulbus arteriosus,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO,GSM8741276,GSM8741276: qKO 5  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq,GSM8741276 r1,GSM8741276,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,10_qKO_B9_R1.fastq.gz,fastq,1749103950.0,23321386.0,GSM8741276 r1,0:75,A:608737363;C:302455983;G:338119173;T:499492171;N:299260,75,,,,608737363,302455983,338119173,499492171,299260,SRX27375413,SRS23810876,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Heart,Cardiovascular System
29146,SRR32025077,SRX27375412,SRS23810877,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,qKO 4  biol rep 1  adult aorta  3 aortas pooled,GSM8741275,,source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing,qKO 4  biol rep 1  adult aorta  3 aortas pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 adult aortas and bulbus arteriosus,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO,GSM8741275,GSM8741275: qKO 4  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq,GSM8741275 r1,GSM8741275,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,9_qKO_A9_R1.fastq.gz,fastq,1391151150.0,18548682.0,GSM8741275 r1,0:75,A:493715157;C:235480005;G:265878909;T:395857913;N:219166,75,,,,493715157,235480005,265878909,395857913,219166,SRX27375412,SRS23810877,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Heart,Cardiovascular System
29147,SRR32025078,SRX27375411,SRS23810875,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,qKO 3  biol rep 1  adult aorta  3 aortas pooled,GSM8741274,,source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing,qKO 3  biol rep 1  adult aorta  3 aortas pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 adult aortas and bulbus arteriosus,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO,GSM8741274,GSM8741274: qKO 3  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq,GSM8741274 r1,GSM8741274,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,8_qKO_H8_R1.fastq.gz,fastq,1548693000.0,20649240.0,GSM8741274 r1,0:75,A:546086416;C:265907989;G:302995102;T:433434795;N:268698,75,,,,546086416,265907989,302995102,433434795,268698,SRX27375411,SRS23810875,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Heart,Cardiovascular System
29148,SRR32025079,SRX27375410,SRS23810873,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,qKO 2  biol rep 1  adult aorta  3 aortas pooled,GSM8741273,,source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing,qKO 2  biol rep 1  adult aorta  3 aortas pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 adult aortas and bulbus arteriosus,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO,GSM8741273,GSM8741273: qKO 2  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq,GSM8741273 r1,GSM8741273,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,7_qKO_G8_R1.fastq.gz,fastq,1420837575.0,18944501.0,GSM8741273 r1,0:75,A:505066296;C:237130175;G:277345211;T:401058536;N:237357,75,,,,505066296,237130175,277345211,401058536,237357,SRX27375410,SRS23810873,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Heart,Cardiovascular System
29149,SRR32025080,SRX27375409,SRS23810874,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,qKO 1  biol rep 1  adult aorta  3 aortas pooled,GSM8741272,,source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO|geo loc name:missing|collection date:missing,qKO 1  biol rep 1  adult aorta  3 aortas pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 adult aortas and bulbus arteriosus,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:qKO,GSM8741272,GSM8741272: qKO 1  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq,GSM8741272 r1,GSM8741272,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,6_qKO_F8_R1.fastq.gz,fastq,1486031025.0,19813747.0,GSM8741272 r1,0:75,A:520876345;C:250796628;G:293184034;T:420907913;N:266105,75,,,,520876345,250796628,293184034,420907913,266105,SRX27375409,SRS23810874,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Heart,Cardiovascular System
29150,SRR32025081,SRX27375408,SRS23810872,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 5  biol rep 1  adult aorta  3 aortas pooled,GSM8741271,,source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing,control 5  biol rep 1  adult aorta  3 aortas pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 adult aortas and bulbus arteriosus,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control,GSM8741271,GSM8741271: control 5  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq,GSM8741271 r1,GSM8741271,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,5_wt_control_E8_R1.fastq.gz,fastq,1415975175.0,18879669.0,GSM8741271 r1,0:75,A:499498659;C:237283969;G:278581269;T:400389063;N:222215,75,,,,499498659,237283969,278581269,400389063,222215,SRX27375408,SRS23810872,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Heart,Cardiovascular System
29151,SRR32025082,SRX27375407,SRS23810871,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 4  biol rep 1  adult aorta  3 aortas pooled,GSM8741270,,source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing,control 4  biol rep 1  adult aorta  3 aortas pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 adult aortas and bulbus arteriosus,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control,GSM8741270,GSM8741270: control 4  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq,GSM8741270 r1,GSM8741270,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,4_wt_control_D8_R1.fastq.gz,fastq,1448565375.0,19314205.0,GSM8741270 r1,0:75,A:515361139;C:240035739;G:286658162;T:406262131;N:248204,75,,,,515361139,240035739,286658162,406262131,248204,SRX27375407,SRS23810871,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Heart,Cardiovascular System
29152,SRR32025083,SRX27375406,SRS23810870,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 3  biol rep 1  adult aorta  3 aortas pooled,GSM8741269,,source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing,control 3  biol rep 1  adult aorta  3 aortas pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 adult aortas and bulbus arteriosus,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control,GSM8741269,GSM8741269: control 3  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq,GSM8741269 r1,GSM8741269,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,3_wt_control_C8_R1.fastq.gz,fastq,1171513275.0,15620177.0,GSM8741269 r1,0:75,A:417371801;C:198042286;G:227929434;T:328006138;N:163616,75,,,,417371801,198042286,227929434,328006138,163616,SRX27375406,SRS23810870,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Heart,Cardiovascular System
29153,SRR32025084,SRX27375405,SRS23810869,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 2  biol rep 1  adult aorta  3 aortas pooled,GSM8741268,,source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing,control 2  biol rep 1  adult aorta  3 aortas pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 adult aortas and bulbus arteriosus,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control,GSM8741268,GSM8741268: control 2  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq,GSM8741268 r1,GSM8741268,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,2_wt_control_B8_R1.fastq.gz,fastq,1379973000.0,18399640.0,GSM8741268 r1,0:75,A:487735196;C:232122567;G:270442978;T:389464154;N:208105,75,,,,487735196,232122567,270442978,389464154,208105,SRX27375405,SRS23810869,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Heart,Cardiovascular System
29154,SRR32025085,SRX27375404,SRS23810868,SRP476805,PRJNA1050594,Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture,GSE249792,Transcriptome Analysis,Thoracic aortic dissection TAD is associated with a high mortality rate. Despite the existence of different mouse models for TAD  the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical diameters as current pharmacological interventions are unable to stop disease progression.  In humans  loss of function LOF of SMAD3 and SMAD6 impair vascular homeostasis  increasing the risk for TAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. We discovered an increased diameter of the ventral aorta in smad3a / ;smad3b /  double knockout zebrafish larvae   while smad6a / ;smad6b /  double knockout  zebrafish have a reduced diameter associated with early mortality. Surprisingly  the smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish model is viable and survives to maturity  although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta showed medial elastolysis and aortic dissections and ruptures at sites exposed to high hemodynamic stress. RNA sequencing of qKO larvae indicated a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis  a previously unaddressed pathway in this pathology. We confirmed that pharmacological modulation of tyrosinase has an effect on aortic morphology. Our study shows that dysregulation of SMAD3/6 dependent signaling has an important impact on thoracic aortic homeostasis  and that using the qKO zebrafish model  thus far the only known model of aortic dissection and rupture in this species  can identify novel pathophysiological pathways leading to TAD. Overall design: For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. One experiment was performed using TruSeq. RNA sequencing was performed on five pools  each containing five smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO zebrafish or wt control cousins.  Only samples with RNA integrity number RIN values higher than 9 were considered. All other experiments were performed using Quantseq. For quantseq sample 1 10  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b / ;smad6a / ;smad6b /  quadruple knockout qKO  adult aortas  and five pools of three wt control cousins aortas. For quantseq sample 11 20  RNA sequencing was performed on five pools  each containing three smad3a / ;smad3b /  double knockout DKO zebrafish or wt control cousins.  For quantseq sample 21 30  RNA sequencing was performed on five pools  each containing three smad6a / ;smad6b /  double knockout DKO zebrafish or wt control cousins.,,,,control 1  biol rep 1  adult aorta  3 aortas pooled,GSM8741267,,source name:pool of 3 adult aortas and bulbus arteriosus|tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control|geo loc name:missing|collection date:missing,control 1  biol rep 1  adult aorta  3 aortas pooled,Raw read QC: UMI and spacer were removed using UMI tools v1.1.4  resulting in raw reads with a remaining length of 65 nt. Raw sequencing reads were inspected using FastQC v0.12.1 for their quality and length. Putative contaminations were checked using FastQ Screen v0.15.3 and a set of genomes of common lab organisms. Read quality based on phred scores is good. Contamination screening reveals that the reads do not map exclusively to any of the other tested organisms. Limited cross mapping to other organisms is normal and caused by homology between organisms. Adapter and quality trimming: Adaptor trimming was done using cutadapt v4.9 with added filtering of reads containing ambiguities or not passing the phred score threshold of 20. The quality of the remaining read pairs was checked using FastQC Read mapping and feature counting: For each sample  trimmed reads were mapped on the zebrafish genome GRCz11  ENSEMBL release 112 using the splice aware STAR v2.7.10a mapper. UMI based deduplication of mapped reads was done with UMI tools v1.1.4. Feature counting at the gene and transcript isoform level was done using rsem calculate expression RSEM v1.3.3. Raw counts for all samples are available as an Excel file. We used the gene level counts for all subsequent analyses. Differential gene expression: Assembly: GRCz11 Supplementary files format and content: Raw counts for all samples are avialable as an Excel file: all samples raw feature counts.xlsx,pool of 3 adult aortas and bulbus arteriosus,,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,Embryos were grown at 27°C in E3 medium with methylene blue until 5 dpf dpf. At 1 dpf and 3 dpf  medium was refreshed. For adults  zebrafish  were housed at the zebrafish facility Ghent in semi closed recirculating housing systems ZebTEC and WTU systems  Tecniplast at a constant temperature 27 28°C  pH 7 5  conductivity 550µS and light dark cycle 14/10. Zebrafish were fed every day with dry food Gemma Micro and with artemia Ocean Nutrition.,tissue:pool of 3 adult aortas and bulbus arteriosus|genotype:wt control,GSM8741267,GSM8741267: control 1  biol rep 1  adult aorta  3 aortas pooled; Danio rerio; RNA Seq,GSM8741267 r1,GSM8741267,1,For RNA extraction  the Rneasy® minikit Qiagen; Hilden  Germany was used following manufacturers guidelines. For each sample  a sequencing library was constructed starting from 16 ng input RNA using the QuantSeq three prime mRNA Seq Library Prep Kit FWD for Illumina Lexogen and the UMI Second Strand Synthesis Module for QuantSeq FWD Illumina  Read 1. This incorporates a unique molecular identifier UMI in the first 6 nucleotides of each read  allowing to identify PCR duplicates and eliminate amplification bias. The libraries were sequenced as single read 75 on an Aviti device Element Biosciences.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ELEMENT,Element AVITI,,SRP476805,,,1_wt_control_A8_R1.fastq.gz,fastq,1068193125.0,14242575.0,GSM8741267 r1,0:75,A:379776425;C:179521683;G:209337737;T:299415096;N:142184,75,,,,379776425,179521683,209337737,299415096,142184,SRX27375404,SRS23810868,SRA2053000,"Callewaert Lab, Biomolecular medicine, Ghent University","Callewaert Lab, Biomolecular medicine, Ghent University",,,,,,,,,,,,B,,usable mapping rate,element,element,3prime,cdna_unspecified,lexogen,bulk,unknown,unknown,,Belgium,2025-01-16,Multi-stage,Multi-stage,Heart,Cardiovascular System
30006,SRR27663958,SRX23331822,SRS20194274,SRP484810,PRJNA1066877,p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation,GSE253758,Transcriptome Analysis,While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.,,pubmed:39242546,,NFKB   biol rep 3,GSM8027552,,tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted|geo loc name:missing|collection date:missing,NFKB   biol rep 3,Data was analyzed by ROSALIND® https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene,endothelial cells,22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.,cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted,GSM8027552,GSM8027552: NFKB   biol rep 3; Danio rerio; RNA Seq,GSM8027552 r1,GSM8027552,1,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484810,,loader:fastq load.py,6-RNA-1001_S6_L001_R1_001.fastq.gz,fastq,7566894200.0,75668942.0,GSM8027552 r1,0:100,A:2055514007;C:1776454819;G:1779667416;T:1955100553;N:157405,100,,,,2055514007,1776454819,1779667416,1955100553,157405,SRX23331822,SRS20194274,SRA1788753,Iowa State University,Iowa State University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-01-19,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
30007,SRR27663959,SRX23331821,SRS20194275,SRP484810,PRJNA1066877,p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation,GSE253758,Transcriptome Analysis,While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.,,pubmed:39242546,,NFKB   biol rep 2,GSM8027551,,tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted|geo loc name:missing|collection date:missing,NFKB   biol rep 2,Data was analyzed by ROSALIND® https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene,endothelial cells,22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.,cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted,GSM8027551,GSM8027551: NFKB   biol rep 2; Danio rerio; RNA Seq,GSM8027551 r1,GSM8027551,1,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484810,,loader:fastq load.py,5-RNA-0901_S5_L001_R1_001.fastq.gz,fastq,8077393600.0,80773936.0,GSM8027551 r1,0:100,A:2195547260;C:1863472493;G:1887149224;T:2131055526;N:169097,100,,,,2195547260,1863472493,1887149224,2131055526,169097,SRX23331821,SRS20194275,SRA1788753,Iowa State University,Iowa State University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-01-19,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
30008,SRR27663960,SRX23331820,SRS20194273,SRP484810,PRJNA1066877,p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation,GSE253758,Transcriptome Analysis,While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.,,pubmed:39242546,,NFKB   biol rep 1,GSM8027550,,tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted|geo loc name:missing|collection date:missing,NFKB   biol rep 1,Data was analyzed by ROSALIND® https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene,endothelial cells,22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.,cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB  sorted,GSM8027550,GSM8027550: NFKB   biol rep 1; Danio rerio; RNA Seq,GSM8027550 r1,GSM8027550,1,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484810,,loader:fastq load.py,4-RNA-1001_S4_L001_R1_001.fastq.gz,fastq,6536957300.0,65369573.0,GSM8027550 r1,0:100,A:1764502914;C:1531091007;G:1533764634;T:1707464708;N:134037,100,,,,1764502914,1531091007,1533764634,1707464708,134037,SRX23331820,SRS20194273,SRA1788753,Iowa State University,Iowa State University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-01-19,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
30009,SRR27663961,SRX23331819,SRS20194272,SRP484810,PRJNA1066877,p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation,GSE253758,Transcriptome Analysis,While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.,,pubmed:39242546,,NFKB+  biol rep 3,GSM8027549,,tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing,NFKB+  biol rep 3,Data was analyzed by ROSALIND® https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene,endothelial cells,22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.,cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted,GSM8027549,GSM8027549: NFKB+  biol rep 3; Danio rerio; RNA Seq,GSM8027549 r1,GSM8027549,1,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484810,,loader:fastq load.py,3-RNA-1001_S3_L001_R1_001.fastq.gz,fastq,10375249700.0,103752497.0,GSM8027549 r1,0:100,A:2873369145;C:2335823279;G:2356855554;T:2808985435;N:216287,100,,,,2873369145,2335823279,2356855554,2808985435,216287,SRX23331819,SRS20194272,SRA1788753,Iowa State University,Iowa State University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-01-19,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
30010,SRR27663962,SRX23331818,SRS20194271,SRP484810,PRJNA1066877,p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation,GSE253758,Transcriptome Analysis,While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.,,pubmed:39242546,,NFKB+  biol rep 2,GSM8027548,,tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing,NFKB+  biol rep 2,Data was analyzed by ROSALIND® https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene,endothelial cells,22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.,cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted,GSM8027548,GSM8027548: NFKB+  biol rep 2; Danio rerio; RNA Seq,GSM8027548 r1,GSM8027548,1,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484810,,loader:fastq load.py,2-RNA-1001_S2_L001_R1_001.fastq.gz,fastq,5743794100.0,57437941.0,GSM8027548 r1,0:100,A:1588561398;C:1297479370;G:1310669617;T:1546965673;N:118042,100,,,,1588561398,1297479370,1310669617,1546965673,118042,SRX23331818,SRS20194271,SRA1788753,Iowa State University,Iowa State University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-01-19,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
30011,SRR27663963,SRX23331817,SRS20194270,SRP484810,PRJNA1066877,p65 signaling dynamics drive the developmental progression of hematopoietic stem and progenitor cells through cell cycle regulation,GSE253758,Transcriptome Analysis,While hematopoietic stem and progenitor cells HSPCs and the signaling pathways that specify them have been well defined in vivo  deriving functional HSPCs from human pluripotent stem cells hPSCs is still an outstanding challenge in the stem cell field. This has impaired efforts to use patient specific HSPCs and their derivatives to treat leukemia  lymphoma  anemia  and solid cancers. Identifying the missing element to derive functional human HSPCs will be critical to advance these therapies. Here  we found that in contrast to in vitro protocols where signaling pathways are typically manipulated statically  the natural developmental progression of HSPC fate in the embryo requires a precise and temporally controlled oscillatory signaling dynamics.  Particularly  our work reveals that NF kB signaling works as an oscillatory clock that controls the developmental progression of HSPCs by driving phases of quiescence and proliferation precisely during embryonic development. This was revealed by live imaging of a custom NF kB zebrafish reporter line  in conjunction with transcriptomic profiling and precise temporal manipulations of the NF kB family member p65  the driver of these signaling events. We also show that in vitro protocols of human hematopoietic differentiation from iPSCs depend on initial pro inflammatory signaling activation. In summary  our results uncover the functional role of pro inflammatory signaling during HSPC specification  revealed their oscillatory dynamics  and define this signaling pathway as the main driver of HSPC fate progression. The integration of these dynamics in vitro will be fundamental to achieve the long standing goal of generating and expanding patient derived functional HSPCs. Overall design: To gain insights into how NF kB in endothelium was contributing to HSPC specification  NFKB+ or NFKB  endothelial cells kdrl+ were sorted and collected from 22hpf zebrafish embryos in triplicate and subject to RNA seq.,,pubmed:39242546,,NFKB+  biol rep 1,GSM8027547,,tissue:endothelial cells|cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted|geo loc name:missing|collection date:missing,NFKB+  biol rep 1,Data was analyzed by ROSALIND® https://rosalind.bio/  with a HyperScale architecture developed by ROSALIND  Inc. San Diego  CA. Reads were trimmed using cutadapt. Reads were aligned to the Danio rerio genome build danRer10 using STAR. Individual sample reads were quantified using HTseq and normalized via Relative Log Expression RLE using DESeq2. Assembly: danRer10 Supplementary files format and content: comma delimited text files include fold change  p values  adjusted p values  and normalized abundance values per sample for each gene,endothelial cells,22hpf NFKB:d2eGFP x kdrl:mCherry zebrafish embryos were screened with Leica M165FC stereomicroscope  dechorionated with pronase Millipore Sigma; 11459643001  anesthetized in 1% tricaine Pentair; TRS5 and dissociated. Specifically  the trunk region of each embryo was surgically isolated posterior to the yolk ball and anterior to the urogenital canal using a scalpel. The collected tissue was then gently vortexed at 28C for 5 20 mins with 50 µg/ml Liberase TM Millipore Sigma: 5401127001 in Dulbecco′s Phosphate Buffered Saline solution with Ca2+ and Mg2+ Millipore Sigma  D8662. The resulting cell suspension was filtered through 30 µm nylon mesh Fisher Scientific; NC9084441 using a 21 gauge syringe Fisher Scientific; BD 309624 and stained with SYTOX™ Red Life Technologies; S34859 to exclude dead cells. Kdrl+/NFKB  and kdrl+/NFKB+ cells were each sorted and collected with BD FACS Aria III. 7 000 cells per sample were collected by FACS in Eppendorf tubes containing 250 µl of RLT buffer.,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer’s instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,Zebrafish Danio rerio embryos and adults were mated  staged  raised  and processed in a circulating aquarium system maintained at 26 °C on a 14 hr light/10 hr dark cycle.,cell type:endothelial cells|genotype:NFKB:d2eGFP x kdrl:mCherry|treatment:kdrl+/NFKB+ sorted,GSM8027547,GSM8027547: NFKB+  biol rep 1; Danio rerio; RNA Seq,GSM8027547 r1,GSM8027547,1,RNA was then isolated and purified with RNeasy® Micro Kit Qiagen. DNase I treatment was performed as specified by the manufacturer. Total RNA was assessed for quality and quantity using an Agilent 2100 Bioanalyzer with RNA 6000 Pico Kit. Triplicate RNA samples of each condition were processed following manufacturer's instructions. Samples were then used to generate RNA sequencing libraries using NEBNext Single Cell/Low Input RNA Library Prep Kit NEB #E6420S/L for Illumina and NEB's Unique Dual Index primers for Illumina E6440.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,SRP484810,,loader:fastq load.py,1-RNA-0917_S1_L001_R1_001.fastq.gz,fastq,6201542500.0,62015425.0,GSM8027547 r1,0:100,A:1696049302;C:1431941155;G:1441395671;T:1632027072;N:129300,100,,,,1696049302,1431941155,1441395671,1632027072,129300,SRX23331817,SRS20194270,SRA1788753,Iowa State University,Iowa State University,,,,,,,,,,,,B,,usable mapping rate,illumina,novaseq_era,unknown,cdna_unspecified,nebnext,bulk,unknown,unknown,,United States,2024-01-19,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33669,SRR30530658,SRX25954305,SRS22536191,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，high glucose,GSM8494124,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，high glucose,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494124,GSM8494124: endothelial cells，high glucose; Danio rerio; RNA Seq,GSM8494124 r1,GSM8494124,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,lr57glu96hpf_R1.fq.gz lr57glu96hpf_R2.fq.gz,fastq fastq,196891371600.0,656304572.0,GSM8494124 r1,0:150 1:150,A:46034913013;C:37262343828;G:60636104680;T:52955473756;N:2536323,150,150,,,46034913013,37262343828,60636104680,52955473756,2536323,SRX25954305,SRS22536191,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33670,SRR30530659,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_1_1_R1.fq.gz SH190424C_LR5796dpf_1_1_R2.fq.gz,fastq fastq,18351420300.0,61171401.0,GSM8494123 r1,0:150 1:150,A:3872504772;C:3434009784;G:6583451920;T:4461384217;N:69607,150,150,,,3872504772,3434009784,6583451920,4461384217,69607,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33671,SRR30530660,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_1_2_R1.fq.gz SH190424C_LR5796dpf_1_2_R2.fq.gz,fastq fastq,36386960400.0,121289868.0,GSM8494123 r2,0:150 1:150,A:8890006445;C:6974694151;G:10814990376;T:9707137150;N:132278,150,150,,,8890006445,6974694151,10814990376,9707137150,132278,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33672,SRR30530661,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_2_1_R1.fq.gz SH190424C_LR5796dpf_2_1_R2.fq.gz,fastq fastq,44811813000.0,149372710.0,GSM8494123 r3,0:150 1:150,A:10939691275;C:8613307673;G:13332283843;T:11926366839;N:163370,150,150,,,10939691275,8613307673,13332283843,11926366839,163370,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33673,SRR30530662,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_2_2_R1.fq.gz SH190424C_LR5796dpf_2_2_R2.fq.gz,fastq fastq,22587582300.0,75291941.0,GSM8494123 r4,0:150 1:150,A:4762937825;C:4235264474;G:8108549401;T:5480746863;N:83737,150,150,,,4762937825,4235264474,8108549401,5480746863,83737,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33674,SRR30530663,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_3_1_R1.fq.gz SH190424C_LR5796dpf_3_1_R2.fq.gz,fastq fastq,31458502200.0,104861674.0,GSM8494123 r5,0:150 1:150,A:7597642424;C:6175910515;G:9377029875;T:8307805635;N:113751,150,150,,,7597642424,6175910515,9377029875,8307805635,113751,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33675,SRR30530664,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_3_2_R1.fq.gz SH190424C_LR5796dpf_3_2_R2.fq.gz,fastq fastq,15812987400.0,52709958.0,GSM8494123 r6,0:150 1:150,A:3317721700;C:3009997461;G:5662825685;T:3822382737;N:59817,150,150,,,3317721700,3009997461,5662825685,3822382737,59817,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33676,SRR30530665,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_4_1_R1.fq.gz SH190424C_LR5796dpf_4_1_R2.fq.gz,fastq fastq,19472976900.0,64909923.0,GSM8494123 r7,0:150 1:150,A:4109297307;C:3636046624;G:6996008921;T:4731548865;N:75183,150,150,,,4109297307,3636046624,6996008921,4731548865,75183,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
33677,SRR30530666,SRX25954304,SRS22536190,SRP530279,PRJNA1156090,Single cell transcriptome sequencing analysis of endothelial cells in control and high glucose treated zebrafish embryos,GSE276251,Transcriptome Analysis,Artificially sweetened beverages containing noncaloric monosaccharides were suggested as healthier alternatives to sugar sweetened beverages. Nevertheless  the potential detrimental effects of these noncaloric monosaccharides on blood vessel function remain inadequately understood. Presently  we have established a zebrafish model that exhibits significant excessive angiogenesis induced by high glucose. Utilizing this model  we observed that glucose and noncaloric monosaccharides could induce excessive formation of blood vessels  especially intersegmental vessels ISVs. The excessively branched vessels were observed to be formed by ectopic activation of quiescent endothelial cells ECs into tip cells. Single cell transcriptomic sequencing analysis of the endothelial cells in the embryos exposed to high glucose revealed an augmented ratio of capillary ECs  proliferating ECs  and a series of upregulated proangiogenic genes. Overall design: Firstly  we isolated the EGFP positive cells from control and high glucose treated Tgfli1ep:EGFP CAAX transgenic embryos. Following the proteolytic dissociation of embryos  the EGFP positive cells were isolated by fluorescence activated cell sorting FACS. Around 300500 zebrafish embryos were used for the ECs collection for each stage. The isolated ECs were analyzed using a large scale scRNA seq 10X Genomics platform.,,pubmed:39365738;pubmed:39882604,,endothelial cells，control,GSM8494123,,tissue:endothelial cells|cell type:endothelial cells|geo loc name:missing|collection date:missing,endothelial cells，control,Cell Ranger 3.0.2 https://github.com/10XGenomics/cellranger was used to convert the raw sequencing data to single cell level gene counts matrix. The clustering of single cells and the marker genes in each cluster were analyzed by Seurat 3.0 https://satijalab.org/seurat/install.html Assembly: The reference genome fasta format and gene annotation gtf format files were downloaded from Ensembl database release version 94. Supplementary files format and content: Tab separated values files and matrix files.,endothelial cells,Embryos were treated with 6% glucose from 24 hpf to 72 hpf.,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell 3’Reagent Kits v3 from 10X Genomics Company.,Tgkdrl:EGFP embryos were raised in E3 solution at 28.5℃ to the indicated developmental stage.,cell type:endothelial cells,GSM8494123,GSM8494123: endothelial cells，control; Danio rerio; RNA Seq,GSM8494123 r1,GSM8494123,1,Embryos were transferred into a 15 mL falcon tube with 10 mL phosphate buffered saline PBS containing 0.25% trypsin and incubated in a rolling machine for 30 min at 28°C during which they were pipetted up and down per 5 min. post centrifuging for 5 min at 800 g at 4°C  cells were resuspended in PBS containing 0.25% trypsin and 15% fetal calf serum FCS to stop the digestion and centrifuged for 5 min at 800 g at 4°C. Cells were rinsed with PBS containing 2% FCS for 2 times and resuspended in PBS. EGFP positive cells were first enriched by fluorescence activated cell sorting FACS  and then went through library preparation following the standard protocol named Chromium Single Cell three primeReagent Kits v3 from 10X Genomics Company.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP530279,,,SH190424C_LR5796dpf_4_2_R1.fq.gz SH190424C_LR5796dpf_4_2_R2.fq.gz,fastq fastq,39005746200.0,130019154.0,GSM8494123 r8,0:150 1:150,A:9542890616;C:7456459618;G:11598648802;T:10407604379;N:142785,150,150,,,9542890616,7456459618,11598648802,10407604379,142785,SRX25954304,SRS22536190,SRA1961613,Nantong University,Nantong University,,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,China,2024-09-03,Multi-stage,Multi-stage,Endothelium,Cardiovascular System
52163,SRR18181443,SRX14328407,SRS12144038,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,Heart2,GSM5924281,,source name:heart|strain:Tubingen|tissue:heart|genotype:wild type,Heart2,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,heart,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:heart|genotype:wild type,GSM5924281,GSM5924281: Heart2; Danio rerio; RNA Seq,GSM5924281,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924281,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Heart2.bam,bam,12289381500.0,40964605.0,GSM5924281 r1,0:150 1:150,A:2992562186;C:2244952830;G:2193151336;T:4856123220;N:2591928,150,150,,,2992562186,2244952830,2193151336,4856123220,2591928,SRX14328407,SRS12144038,SRA880843,GEO,Zhejiang University,2,0.0,0.78893,0.0,0.01228,1.0,0.91441,,0.62655,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Heart,Cardiovascular System
52164,SRR18181442,SRX14328406,SRS12144037,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,Heart1,GSM5924280,,source name:heart|strain:Tubingen|tissue:heart|genotype:wild type,Heart1,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Mus musculus.GRCm38.88 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,heart,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|tissue:heart|genotype:wild type,GSM5924280,GSM5924280: Heart1; Danio rerio; RNA Seq,GSM5924280,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM5924280,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10|intentional duplicate,Heart1.bam,bam,8428658100.0,28095527.0,GSM5924280 r1,0:150 1:150,A:2058121249;C:1561350035;G:1570099343;T:3238195048;N:892425,150,150,,,2058121249,1561350035,1570099343,3238195048,892425,SRX14328406,SRS12144037,SRA880843,GEO,Zhejiang University,2,2e-05,0.88435,0.0,0.01173,0.99997,0.89045,1.0,0.54187,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2022-03-01,Undetermined,Multi-stage,Heart,Cardiovascular System
52188,SRR9058959,SRX5835159,SRS4761455,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,Heart4,GSM3768156,,source name:heart|strain:Tubingen|genotype/variation:wild type|tissue:heart,Heart4,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,heart,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:heart,GSM3768156,GSM3768156: Heart4; Danio rerio; RNA Seq,GSM3768156,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768156,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Heart4.bam,bam,52461585418.0,173713859.0,GSM3768156 r1,0:151 1:151,A:12784605546;C:9053648554;G:9236590524;T:21249234138;N:137506656,151,151,,,12784605546,9053648554,9236590524,21249234138,137506656,SRX5835159,SRS4761455,SRA880843,GEO,Zhejiang University,2,0.0,0.77522,0.0,0.03304,1.0,0.85632,,0.55248,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Heart,Cardiovascular System
52189,SRR9058958,SRX5835158,SRS4761454,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,Heart3,GSM3768155,,source name:heart|strain:Tubingen|genotype/variation:wild type|tissue:heart,Heart3,Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: Danio rerio GRCz10 Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,heart,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype/variation:wild type|tissue:heart,GSM3768155,GSM3768155: Heart3; Danio rerio; RNA Seq,GSM3768155,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3768155,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:http://dec2017.archive.ensembl.org/Danio rerio/Info/Index,Heart3.bam,bam,23533995978.0,77927139.0,GSM3768155 r1,0:151 1:151,A:6051087690;C:3978622675;G:3909835641;T:9588867829;N:5582143,151,151,,,6051087690,3978622675,3909835641,9588867829,5582143,SRX5835158,SRS4761454,SRA880843,GEO,Zhejiang University,2,0.0,0.74298,0.0,0.02452,1.0,0.88107,,0.61909,151,151,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-05-15,Undetermined,Multi-stage,Heart,Cardiovascular System
52206,SRR8991399,SRX5770467,SRS4704576,SRP194254,PRJNA540466,Characterization of the zebrafish cell landscape at single cell resolution,GSE130487,Transcriptome Analysis,Zebrafish have been found to be a premier model organism in biological and regeneration research. However  the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here  we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall  our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1  2022.,,pubmed:34660600,,Heart5,GSM3740952,,source name:heart|strain:Tubingen|genotype:wild type|tissue:heart,Heart5,The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a  with default configurations. Next  merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last  we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts  columns are cells  and rows are genes.,heart,,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,,strain:Tubingen|genotype:wild type|tissue:heart,GSM3740952,GSM3740952: Heart5; Danio rerio; RNA Seq,GSM3740952,,1,Tissue dissociation and  single cell lysate Library preparations were performed with the Microwell seq protocol,GEO Accession:GSM3740952,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq X Ten,,SRP194254,,assembly:Danio rerio GRCz10,Heart5.bam,bam,43163633400.0,143878778.0,GSM3740952 r1,0:150 1:150,A:9349719585;C:8099097553;G:8061219131;T:17651447621;N:2149510,150,150,,,9349719585,8099097553,8061219131,17651447621,2149510,SRX5770467,SRS4704576,SRA880843,GEO,Zhejiang University,2,0.0,0.78756,0.0,0.01363,1.0,0.8994,,0.4146,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_plate,microwellseq,,China,2019-04-30,Undetermined,Multi-stage,Heart,Cardiovascular System
55365,SRR10321288,SRX7032108,SRS5552214,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK2,GSM4134187,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK2,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134187,GSM4134187: FK2; Danio rerio; RNA Seq,GSM4134187,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134187,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,Fk-2_H3MHFBGXY_S4_L001_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L001_R2_001.fastq.gz,fastq fastq,2747645940.0,18195462.0,GSM4134187 r1,0:75.51 1:75.50,A:761850296;C:390951746;G:422952266;T:1169751842;N:2139790,75,75,,,761850296,390951746,422952266,1169751842,2139790,SRX7032108,SRS5552214,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.23534,0.89135,0.19366,0.15359,0.99902,0.86636,0.40119,0.71094,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55366,SRR10321289,SRX7032108,SRS5552214,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK2,GSM4134187,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK2,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134187,GSM4134187: FK2; Danio rerio; RNA Seq,GSM4134187,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134187,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,Fk-2_H3MHFBGXY_S4_L002_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L002_R2_001.fastq.gz,fastq fastq,2719577388.0,18010558.0,GSM4134187 r2,0:75.50 1:75.50,A:750500832;C:383761329;G:435629268;T:1147504474;N:2181485,75,75,,,750500832,383761329,435629268,1147504474,2181485,SRX7032108,SRS5552214,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.21913,0.88799,0.16554,0.15559,0.99855,0.8704,0.48175,0.71083,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55367,SRR10321290,SRX7032108,SRS5552214,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK2,GSM4134187,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK2,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134187,GSM4134187: FK2; Danio rerio; RNA Seq,GSM4134187,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134187,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,Fk-2_H3MHFBGXY_S4_L003_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L003_R2_001.fastq.gz,fastq fastq,2396848795.0,15867573.0,GSM4134187 r3,0:75.56 1:75.50,A:649358056;C:340829352;G:366620430;T:1039511314;N:529643,75,75,,,649358056,340829352,366620430,1039511314,529643,SRX7032108,SRS5552214,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.22581,0.89171,0.18682,0.15894,0.99928,0.87054,0.41592,0.70495,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55368,SRR10321291,SRX7032108,SRS5552214,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK2,GSM4134187,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK2,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134187,GSM4134187: FK2; Danio rerio; RNA Seq,GSM4134187,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134187,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,Fk-2_H3MHFBGXY_S4_L004_R1_001.fastq.gz Fk-2_H3MHFBGXY_S4_L004_R2_001.fastq.gz,fastq fastq,2610671390.0,17282452.0,GSM4134187 r4,0:75.56 1:75.50,A:691899084;C:368646569;G:415634004;T:1133907995;N:583738,75,75,,,691899084,368646569,415634004,1133907995,583738,SRX7032108,SRS5552214,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.24107,0.8886,0.19934,0.15491,0.99926,0.8702,0.31578,0.66998,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55369,SRR10321284,SRX7032107,SRS5552213,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK1,GSM4134186,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK1,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134186,GSM4134186: FK1; Danio rerio; RNA Seq,GSM4134186,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134186,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,FK-1_H3MHFBGXY_S3_L001_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L001_R2_001.fastq.gz,fastq fastq,2366670719.0,15672127.0,GSM4134186 r1,0:75.50 1:75.51,A:648000254;C:343663478;G:358343004;T:1014831853;N:1832130,75,75,,,648000254,343663478,358343004,1014831853,1832130,SRX7032107,SRS5552213,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.30353,0.90485,0.25842,0.14878,0.99912,0.85857,0.23863,0.71645,76,75,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55370,SRR10321285,SRX7032107,SRS5552213,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK1,GSM4134186,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK1,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134186,GSM4134186: FK1; Danio rerio; RNA Seq,GSM4134186,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134186,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,FK-1_H3MHFBGXY_S3_L002_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L002_R2_001.fastq.gz,fastq fastq,2360571906.0,15632617.0,GSM4134186 r2,0:75.49 1:75.51,A:643644738;C:339965378;G:371359828;T:1003716606;N:1885356,75,75,,,643644738,339965378,371359828,1003716606,1885356,SRX7032107,SRS5552213,SRA982819,GEO,"Bakkers, Hubrecht Institute",,,,,,,,,,,,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55371,SRR10321286,SRX7032107,SRS5552213,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK1,GSM4134186,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK1,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134186,GSM4134186: FK1; Danio rerio; RNA Seq,GSM4134186,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134186,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,FK-1_H3MHFBGXY_S3_L003_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L003_R2_001.fastq.gz,fastq fastq,2074411223.0,13732357.0,GSM4134186 r3,0:75.55 1:75.51,A:554276583;C:300804770;G:312025485;T:906833457;N:470928,75,75,,,554276583,300804770,312025485,906833457,470928,SRX7032107,SRS5552213,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.2996,0.90397,0.25521,0.15245,0.99933,0.86314,0.21969,0.69653,75,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
55372,SRR10321287,SRX7032107,SRS5552213,SRP226527,PRJNA578764,Single cell analysis uncovers that metabolic reprogramming is essential for cardiomyocyte proliferation in the regenerating heart.,GSE139218,Transcriptome Analysis,While the heart regenerates poorly in mammals  efficient heart regeneration occurs in certain amphibian and fish species. Zebrafish has been used extensively to study heart regeneration  resulting in a model in which preexisting cardiomyocytes dedifferentiate and reinitiate proliferation to replace the lost myocardium. However  there is limited knowledge about the cellular processes that occur in this rare population of proliferating cardiomyocytes during heart regeneration. To identify such processes  we generated a transgenic line based on nppa expression that marks proliferating cardiomyocytes located at the wound border zone.  Next we have used a single cell RNA sequencing approach in the regenerating adult zebrafish heart and we uncovered that proliferating border zone cardiomyocytes have very distinct transcriptomes compared to the non proliferating remote cardiomyocytes and that they resemble embryonic cardiomyocytes. Moreover  these cells have reduced expression of mitochondrial genes and reduced mitochondrial oxidative phosphorylation activity  while glycolysis gene expression and glucose uptake are increased  indicative for metabolic reprogramming. Mechanistically  this metabolic reprogramming is induced by Nrg1/Erbb2 signaling and this mechanism is conserved in murine hearts.  Furthermore  pharmacological inhibition of glycolysis impairs cardiomyocyte proliferation of both zebrafish and murine cardiomyocytes. Together these results reveal a conserved mechanism in which cardiomyocytes undergo metabolic reprogramming  which is essential for cardiomyocyte proliferation and heart regeneration and could ultimately help to develop novel methods to promote mammalian heart repair. Overall design: Tgnppa:mCitrine  positive cells  n=576 were collected from 13 cryoinjured hearts. As an internal control  also nppa negative cells were sorted. n=192. In addition Tgmyl7:GFP positive cells n=768 were sorted from 2dpf embryos. All cells were sent for single cell RNA sequencing.,,pubmed:31868166,,FK1,GSM4134186,,source name:Tgnppa:mCitrine ventricle 7dpi|Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,FK1,"Paired end reads were aligned to the transcriptome using bwa version 0.6.2 with default parameters. The zebrafish transcriptome was based on genome release zv9 and contained improved gene annotations as described in Junker et al. 2014 Cell. Sample 1 2 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 4bp unique molecular identifier UMI and followed by a 24 nt PolyA stretch and a number <40 of transcript derived bases. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv""  well numbers refer to the 384 well plate in the following ordre: A1 to A24   B1 to B24 and so on until P24.  Read 1 was not used for quantification. Read 2  containing the right mate of each read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Sample 3 4 Mapped reads were assigned to cells based on barcodes according to the CEL seq2 protocol Hashimshony et al.  2016 In brief  read 1 contains the barcode information: the first eight bases correspond to a cell specific barcode followed by a 6bp unique molecular identifier UMI and followed by a 12 ntPolyA stretch. Cell specific barcodes are specified in the file ""cel seq2 barcodes.csv"".  Read 1 was not used for quantification. Read 2  containing 62nt read pair was mapped to the ensemble ID of all gene loci. Reads mapping to multiple loci were discarded. Genome build: zv9 with improved three prime annotation  see Junker et al 2014 Cell Supplementary files format and content: text files: read count matrices in which rows correspond to genes and  columns to single cells.",Tgnppa:mCitrine ventricle 7dpi,Unfixed ventricles were dissociated by Collagenase and TrypLE Express treatment to prepare single cell solutions.  Samples 1 2 Transgenic tgmyl7:GFP 2dpf embryos n=200 were dechorionated and digested in Ca2+/Mg2+ free HBSS containing Collagenase  followed by TrypLE express treatement. Samples 3 4 Cells were subsequently FACS sorted based on nppa:mCitrine or myl7:GFP expression in 384 well plates  each well containing 1 cell.,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,,Stage:7dpi|line:Tgnppa:mCitrine|tissue:Adult zebrafish ventricle,GSM4134186,GSM4134186: FK1; Danio rerio; RNA Seq,GSM4134186,,1,Live cells were sorted into 384 well plates with Vapor Lock oil containing a droplet with barcoded primers  spike in RNA and dNTPs  followed by heat induced cell lysis and cDNA syntheses using a robotic liquid handler. post cell lysis for 5 minutes at 65C  RT and second strand mixes were distributed with the Nanodrop II liquid handling platform. Primers consisted of a 24bp polyT stretch  a 4bp random molecular barcode UMI  a cell specific 8bp barcode  the five prime Illumina Truseq small RNA kit adapter and a T7 promoter. post all cells were pooled in one library  the CEL seq2 protocol was used for librabry prep Hashimony et al.  2016,GEO Accession:GSM4134186,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP226527,,,FK-1_H3MHFBGXY_S3_L004_R1_001.fastq.gz FK-1_H3MHFBGXY_S3_L004_R2_001.fastq.gz,fastq fastq,2267459781.0,15009993.0,GSM4134186 r4,0:75.55 1:75.51,A:592957170;C:326713096;G:354670327;T:992614149;N:505039,75,75,,,592957170,326713096,354670327,992614149,505039,SRX7032107,SRS5552213,SRA982819,GEO,"Bakkers, Hubrecht Institute",2,0.3137,0.9006,0.26295,0.14953,0.99914,0.8622,0.19895,0.70141,76,76,T,B,mate1 technical by mapping diff,illumina,nextseq,unknown,poly_a,trueseq,sc,single_cell_plate,celseq,,Netherlands,2019-10-21,Multi-stage,Multi-stage,Heart,Cardiovascular System
66207,SRR16097999,SRX12384068,SRS10354360,SRP339110,PRJNA767032,Amino acid primed mTOR activity is essential for heart regeneration [scRNA seq],GSE184914,Transcriptome Analysis,Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes.  Curiously  mouse neonates and zebrafish  larvae or adult  are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation.  However  a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood.  Here  we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate.  Zebrafish and neonatal mouse hearts display elevated glutamine levels  predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing  LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator  TOR primed state  in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed single cell RNA seq of zebrafish heart pre injury  and 3  7 xxx post injury,parent bioproject:PRJNA778001,pubmed:34988408,,zebrafish day 7,GSM5600324,,source name:Zebrafish heart|tissue:heart|strain:AB|time:xxx post injury,zebrafish day 7,Raw reads were processed using the CellRanger software from 10X genomics using recommended default settings. Monocle version 3 alpha was used for single cell RNA seq data analysis and visualization. We kept cells with at least 200 expressed genes  and 1000 Unique Molecular Identifiers UMIs  and less than 40% reads mapped to mitochondrial transcripts. Genome build: GRCz10 Supplementary files format and content: tab delimited file of normalized gene level read counts for each cell,Zebrafish heart,All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation  fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals  7.5 mM MTZ was used.  Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ  3  7  12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described [68  69]. 6 hearts  3 males and 3 females  were isolated from Adult UI  3 dpi and 7 dpi zebrafish.  Each group had 2 sets of samples of 3 hearts each for the digestion process.  Each set of 3 hearts were single celled as previously described [79].  All cells per group were then pooled and sent for sequencing.,Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total  2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart  141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis  reverse transcription  cDNA amplification  and library preparation with indexing per the manufacturer’s protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc.  San Diego  CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.,Wild type AB; Zebrafish International Resource Center  Eugene  OR  USA    hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] [19] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] [5] were used and maintained using standard procedures [67] in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C  pH of 7.5  conductivity of 800 µS  hardness of 140 ppm  alkalinity of 35 ppm  dissolved oxygen content of 7.8 mg/L  and a total gas pressure of 101%. The average nitrate level is 55 ppm  the average nitrite level is 0.05 ppm  and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet  at 12 dpf live artemia is added to the diet  and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.,tissue:heart|strain:AB|time:xxx post injury,GSM5600324,GSM5600324: zebrafish day 7; Danio rerio; RNA Seq,GSM5600324 r1,GSM5600324,1,Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total  2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart  141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis  reverse transcription  cDNA amplification  and library preparation with indexing per the manufacturer's protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc.  San Diego  CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP339110,,assembly:GRCz10|intentional duplicate,zf_7db_possorted_genome_bam.bam,10X Genomics bam file,38062513314.0,388392993.0,GSM5600324 r1,0:98,A:11679656809;C:7784611418;G:8037807349;T:10544896124;N:15541614,98,,,,11679656809,7784611418,8037807349,10544896124,15541614,SRX12384068,SRS10354360,SRA1301815,Institute for Stem Cell and Regenerative Medicine,Institute for Stem Cell and Regenerative Medicine,1,0.93286,,0.08896,,0.87237,,0.56993,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-09-28,Multi-stage,Multi-stage,Heart,Cardiovascular System
66208,SRR16098000,SRX12384067,SRS10354361,SRP339110,PRJNA767032,Amino acid primed mTOR activity is essential for heart regeneration [scRNA seq],GSE184914,Transcriptome Analysis,Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes.  Curiously  mouse neonates and zebrafish  larvae or adult  are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation.  However  a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood.  Here  we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate.  Zebrafish and neonatal mouse hearts display elevated glutamine levels  predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing  LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator  TOR primed state  in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed single cell RNA seq of zebrafish heart pre injury  and 3  7 xxx post injury,parent bioproject:PRJNA778001,pubmed:34988408,,zebrafish day 3,GSM5600323,,source name:Zebrafish heart|tissue:heart|strain:AB|time:xxx post injury,zebrafish day 3,Raw reads were processed using the CellRanger software from 10X genomics using recommended default settings. Monocle version 3 alpha was used for single cell RNA seq data analysis and visualization. We kept cells with at least 200 expressed genes  and 1000 Unique Molecular Identifiers UMIs  and less than 40% reads mapped to mitochondrial transcripts. Genome build: GRCz10 Supplementary files format and content: tab delimited file of normalized gene level read counts for each cell,Zebrafish heart,All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation  fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals  7.5 mM MTZ was used.  Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ  3  7  12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described [68  69]. 6 hearts  3 males and 3 females  were isolated from Adult UI  3 dpi and 7 dpi zebrafish.  Each group had 2 sets of samples of 3 hearts each for the digestion process.  Each set of 3 hearts were single celled as previously described [79].  All cells per group were then pooled and sent for sequencing.,Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total  2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart  141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis  reverse transcription  cDNA amplification  and library preparation with indexing per the manufacturer’s protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc.  San Diego  CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.,Wild type AB; Zebrafish International Resource Center  Eugene  OR  USA    hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] [19] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] [5] were used and maintained using standard procedures [67] in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C  pH of 7.5  conductivity of 800 µS  hardness of 140 ppm  alkalinity of 35 ppm  dissolved oxygen content of 7.8 mg/L  and a total gas pressure of 101%. The average nitrate level is 55 ppm  the average nitrite level is 0.05 ppm  and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet  at 12 dpf live artemia is added to the diet  and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.,tissue:heart|strain:AB|time:xxx post injury,GSM5600323,GSM5600323: zebrafish day 3; Danio rerio; RNA Seq,GSM5600323 r1,GSM5600323,1,Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total  2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart  141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis  reverse transcription  cDNA amplification  and library preparation with indexing per the manufacturer's protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc.  San Diego  CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP339110,,assembly:GRCz10|intentional duplicate,zf_3db_possorted_genome_bam.bam,10X Genomics bam file,35567557578.0,362934261.0,GSM5600323 r1,0:98,A:11273935957;C:7072680901;G:7397087735;T:9812130858;N:11722127,98,,,,11273935957,7072680901,7397087735,9812130858,11722127,SRX12384067,SRS10354361,SRA1301815,Institute for Stem Cell and Regenerative Medicine,Institute for Stem Cell and Regenerative Medicine,1,0.91795,,0.07118,,0.87418,,0.58423,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-09-28,Multi-stage,Multi-stage,Heart,Cardiovascular System
66209,SRR16098001,SRX12384066,SRS10354359,SRP339110,PRJNA767032,Amino acid primed mTOR activity is essential for heart regeneration [scRNA seq],GSE184914,Transcriptome Analysis,Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes.  Curiously  mouse neonates and zebrafish  larvae or adult  are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation.  However  a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood.  Here  we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate.  Zebrafish and neonatal mouse hearts display elevated glutamine levels  predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing  LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator  TOR primed state  in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed single cell RNA seq of zebrafish heart pre injury  and 3  7 xxx post injury,parent bioproject:PRJNA778001,pubmed:34988408,,zebrafish day x,GSM5600322,,source name:Zebrafish heart|tissue:heart|strain:AB|time:0d,zebrafish day x,Raw reads were processed using the CellRanger software from 10X genomics using recommended default settings. Monocle version 3 alpha was used for single cell RNA seq data analysis and visualization. We kept cells with at least 200 expressed genes  and 1000 Unique Molecular Identifiers UMIs  and less than 40% reads mapped to mitochondrial transcripts. Genome build: GRCz10 Supplementary files format and content: tab delimited file of normalized gene level read counts for each cell,Zebrafish heart,All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation  fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals  7.5 mM MTZ was used.  Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ  3  7  12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described [68  69]. 6 hearts  3 males and 3 females  were isolated from Adult UI  3 dpi and 7 dpi zebrafish.  Each group had 2 sets of samples of 3 hearts each for the digestion process.  Each set of 3 hearts were single celled as previously described [79].  All cells per group were then pooled and sent for sequencing.,Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total  2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart  141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis  reverse transcription  cDNA amplification  and library preparation with indexing per the manufacturer’s protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc.  San Diego  CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.,Wild type AB; Zebrafish International Resource Center  Eugene  OR  USA    hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] [19] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] [5] were used and maintained using standard procedures [67] in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C  pH of 7.5  conductivity of 800 µS  hardness of 140 ppm  alkalinity of 35 ppm  dissolved oxygen content of 7.8 mg/L  and a total gas pressure of 101%. The average nitrate level is 55 ppm  the average nitrite level is 0.05 ppm  and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet  at 12 dpf live artemia is added to the diet  and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.,tissue:heart|strain:AB|time:0d,GSM5600322,GSM5600322: zebrafish day x; Danio rerio; RNA Seq,GSM5600322 r1,GSM5600322,1,Cells were resuspended in PBS containing 0.04% BSA at a concentration of 2600 cells/ 33.8 μL solution. In total  2600 cells per sample were loaded into each well of a 10X Chromium single cell capture chip with a recovery of 272 cells for uninjured heart  141 cells for 3 xxx post injury and 368 cells for 7 xxx post injury sample. The captured cells then underwent lysis  reverse transcription  cDNA amplification  and library preparation with indexing per the manufacturer's protocol 10X Genomics. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc.  San Diego  CA using a high output 150 cycle kit with read lengths recommended by 10X Genomics.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP339110,,assembly:GRCz10|intentional duplicate,zf_0db_possorted_genome_bam.bam,10X Genomics bam file,37627884490.0,383958005.0,GSM5600322 r1,0:98,A:12219568490;C:7567146496;G:7074688134;T:10754586205;N:11895165,98,,,,12219568490,7567146496,7074688134,10754586205,11895165,SRX12384066,SRS10354359,SRA1301815,Institute for Stem Cell and Regenerative Medicine,Institute for Stem Cell and Regenerative Medicine,1,0.90337,,0.0832,,0.88562,,0.62367,,98,,B,,usable mapping rate,illumina,hiseq_era,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,United States,2021-09-28,Multi-stage,Multi-stage,Heart,Cardiovascular System
66860,SRR16784084,SRX12983052,SRS10923148,SRP344669,PRJNA778003,Amino acid primed mTOR activity is essential for heart regeneration [bulk RNA seq],GSE188243,Transcriptome Analysis,Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously  mouse neonates and zebrafish  larvae or adult  are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation. However  a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood. Here  we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate. Zebrafish and neonatal mouse hearts display elevated glutamine levels  predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing  LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator  TOR primed state  in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed bulk RNA seq of zebrafish heart at embryonic/fetal day 3  adult control  and 3  and 7 xxx post injury.,parent bioproject:PRJNA778001,pubmed:34988408,,Young day 3 heart   2,GSM5673295,,source name:Zebrafish heart|tissue:Heart|age:Young|treatment:N1|time point:N1,Young day 3 heart   2,Raw reads were aligned to Ensembl GRCz10 using Tophat version 2.0.13. Gene level read counts were quantified using htseq count using Ensembl GRCz10 gene annotations. Genome build: GRCz10 Supplementary files format and content: zebrafish bulk RNAseq count matrix.txt: Tab delimited text file of counts. Supplementary files format and content: zebrafish bulk RNAseq 0 3 7 DPI reads per million.txt: Tab delimited text file of normalized gene level read counts for each cell.,Zebrafish heart,All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation  fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals  7.5 mM MTZ was used. Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ  3  7  12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described. 6 hearts  3 males and 3 females  were isolated from Adult UI  3 dpi and 7 dpi zebrafish. Each group had 2 sets of samples of 3 hearts each for the digestion process. Each set of 3 hearts were single celled as previously described. All cells per group were then pooled and sent for sequencing.,For young  3 dpf zebrafish heart samples  we sequenced N=2 with about n=500 hearts pooled. For the adult heart samples  we sequenced N=2 hearts at UI  3 and 7 dpi with each n=4 6 pooled hearts. A negative binomial test was performed to determine significantly changed genes. Around 20 000 genes were found. RNA was isolated from young 3 dpf  adult 6 mpf  and regenerating 3 and 7 dpi zebrafish hearts as per manufacturers’ protocol TRIzol  ThermoFisher. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc.  San Diego  CA.,Wild type AB; Zebrafish International Resource Center  Eugene  OR  USA  hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] were used and maintained using standard procedures in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C  pH of 7.5  conductivity of 800 µS  hardness of 140 ppm  alkalinity of 35 ppm  dissolved oxygen content of 7.8 mg/L  and a total gas pressure of 101%. The average nitrate level is 55 ppm  the average nitrite level is 0.05 ppm  and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet  at 12 dpf live artemia is added to the diet  and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.,tissue:Heart|age:Young|treatment:N1|time point:N1,GSM5673295,GSM5673295: Young day 3 heart   2; Danio rerio; RNA Seq,GSM5673295,,1,For young  3 dpf zebrafish heart samples  we sequenced N=2 with about n=500 hearts pooled. For the adult heart samples  we sequenced N=2 hearts at UI  3 and 7 dpi with each n=4 6 pooled hearts. A negative binomial test was performed to determine significantly changed genes. Around 20 000 genes were found. RNA was isolated from young 3 dpf  adult 6 mpf  and regenerating 3 and 7 dpi zebrafish hearts as per manufacturers' protocol TRIzol  ThermoFisher. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc.  San Diego  CA.,GEO Accession:GSM5673295,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP344669,,,AC7N1CANXX_US-1555478_CGATGT_L004_R1_001.fastq.gz AC7N1CANXX_US-1555478_CGATGT_L004_R2_001.fastq.gz,fastq fastq,2665083132.0,26128266.0,GSM5673295 r1,0:51 1:51,A:715891096;C:622224275;G:609975907;T:716605393;N:386461,51,51,,,715891096,622224275,609975907,716605393,386461,SRX12983052,SRS10923148,SRA1323644,GEO,Institute for Stem Cell and Regenerative Medicine,2,0.91482,0.91614,0.09011,0.091,0.70043,0.70483,0.50654,0.48799,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-11-04,Multi-stage,Multi-stage,Heart,Cardiovascular System
66861,SRR16784083,SRX12983051,SRS10923147,SRP344669,PRJNA778003,Amino acid primed mTOR activity is essential for heart regeneration [bulk RNA seq],GSE188243,Transcriptome Analysis,Heart disease is the leading cause of death as there is no current method to repair damaged myocardium due to the limited proliferative capacity of adult cardiomyocytes. Curiously  mouse neonates and zebrafish  larvae or adult  are able to regenerate their hearts via cardiomyocyte de differentiation and proliferation. However  a molecular mechanism of why these cardiomyocytes can re enter cell cycle is poorly understood. Here  we identify a unique metabolic state that primes adult zebrafish and neonatal mouse ventricular cardiomyocytes to proliferate. Zebrafish and neonatal mouse hearts display elevated glutamine levels  predisposing them to amino acid driven activation of TOR. We show that this TOR activation is required for zebrafish cardiomyocyte regeneration in vivo. post injury we observe pS6 in both the epicardium and ventricular cardiomyocytes suggesting these are amino acid primed cells necessary for regeneration. Through single cell and system wide RNA sequencing  LQC proteomics and microscopy we identify dramatic metabolic and mitochondrial changes during the first week of regeneration. These data suggest that regeneration of zebrafish myocardium is driven by metabolic remodeling and reveals a unique metabolic regulator  TOR primed state  in which zebrafish and mammalian cardiomyocytes are regeneration competent. Overall design: We performed bulk RNA seq of zebrafish heart at embryonic/fetal day 3  adult control  and 3  and 7 xxx post injury.,parent bioproject:PRJNA778001,pubmed:34988408,,Young day 3 heart   1,GSM5673294,,source name:Zebrafish heart|tissue:Heart|age:Young|treatment:N1|time point:N1,Young day 3 heart   1,Raw reads were aligned to Ensembl GRCz10 using Tophat version 2.0.13. Gene level read counts were quantified using htseq count using Ensembl GRCz10 gene annotations. Genome build: GRCz10 Supplementary files format and content: zebrafish bulk RNAseq count matrix.txt: Tab delimited text file of counts. Supplementary files format and content: zebrafish bulk RNAseq 0 3 7 DPI reads per million.txt: Tab delimited text file of normalized gene level read counts for each cell.,Zebrafish heart,All chemical ventricular cardiomyocyte VCM ablation were conducted on adult Zebrafish 5 mpf 12 mpf. For chemical mediated VCM ablation  fish were treated with 5 mM Metronidiazole MTZ; Sigma containing 0.1% dimethyl sulfoxide DMSO or vehicle control 0.1% DMSO for 48 hours protected from light and refreshed every 24 hours. For Wnt and DKK heat shock heterozygous animals  7.5 mM MTZ was used. Following chemical treatment fish were placed back in original aquaria and hearts were collected at 0 prior to MTZ  3  7  12 and 30 xxx post injury dpi. Larval hearts 72 hpf were isolated and pooled as previously described. 6 hearts  3 males and 3 females  were isolated from Adult UI  3 dpi and 7 dpi zebrafish. Each group had 2 sets of samples of 3 hearts each for the digestion process. Each set of 3 hearts were single celled as previously described. All cells per group were then pooled and sent for sequencing.,For young  3 dpf zebrafish heart samples  we sequenced N=2 with about n=500 hearts pooled. For the adult heart samples  we sequenced N=2 hearts at UI  3 and 7 dpi with each n=4 6 pooled hearts. A negative binomial test was performed to determine significantly changed genes. Around 20 000 genes were found. RNA was isolated from young 3 dpf  adult 6 mpf  and regenerating 3 and 7 dpi zebrafish hearts as per manufacturers’ protocol TRIzol  ThermoFisher. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc.  San Diego  CA.,Wild type AB; Zebrafish International Resource Center  Eugene  OR  USA  hsWnt8:GFP [Tghsp70l:Wnt8a GFPw34] and hsDKK1:GFP [Tghsp70l:DKK1b GFPw32] and vmhc:mCherry NTR [Tgvmhc:mCherry Eco.NfsB] were used and maintained using standard procedures in accordance with the Institutional Animal Care and Use Committee approved protocols IACUC 2057 01 & 4364 02. Reverse osmosis system water is used and the water chemistry was adjusted to a temperature of 27.5°C  pH of 7.5  conductivity of 800 µS  hardness of 140 ppm  alkalinity of 35 ppm  dissolved oxygen content of 7.8 mg/L  and a total gas pressure of 101%. The average nitrate level is 55 ppm  the average nitrite level is 0.05 ppm  and the average ammonium level is 0.01 ppm. Larval feed starting at 5 dpf dpf is a rotifer polyculture supplemented with the Zeigler larval diet  at 12 dpf live artemia is added to the diet  and at 60 dpf 90 dpf the fish are started on the Zeigler adult diet supplemented with live artemia once per day. The health status of the colony showed low presence of pseudoloma neurophilia and an extremely low presence of mycobacterium spp. with no major clinical or subclinical findings of significance.,tissue:Heart|age:Young|treatment:N1|time point:N1,GSM5673294,GSM5673294: Young day 3 heart   1; Danio rerio; RNA Seq,GSM5673294,,1,For young  3 dpf zebrafish heart samples  we sequenced N=2 with about n=500 hearts pooled. For the adult heart samples  we sequenced N=2 hearts at UI  3 and 7 dpi with each n=4 6 pooled hearts. A negative binomial test was performed to determine significantly changed genes. Around 20 000 genes were found. RNA was isolated from young 3 dpf  adult 6 mpf  and regenerating 3 and 7 dpi zebrafish hearts as per manufacturers' protocol TRIzol  ThermoFisher. The libraries were sequenced together on an Illumina HiSeq 4000 Illumina Inc.  San Diego  CA.,GEO Accession:GSM5673294,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,ILLUMINA,Illumina HiSeq 4000,,SRP344669,,,AC7N1CANXX_US-1555441_ATCACG_L004_R1_001.fastq.gz AC7N1CANXX_US-1555441_ATCACG_L004_R2_001.fastq.gz,fastq fastq,2366795862.0,23203881.0,GSM5673294 r1,0:51 1:51,A:635884570;C:553068492;G:541587629;T:635923836;N:331335,51,51,,,635884570,553068492,541587629,635923836,331335,SRX12983051,SRS10923147,SRA1323644,GEO,Institute for Stem Cell and Regenerative Medicine,2,0.91339,0.91347,0.08746,0.08855,0.70278,0.70822,0.49649,0.49352,51,51,B,B,biological fallback assumption,illumina,hiseq_era,unknown,cdna_unspecified,unknown,bulk,bulk,bulk,,United States,2021-11-04,Multi-stage,Multi-stage,Heart,Cardiovascular System
71060,SRR21218371,SRX17229108,SRS14795574,SRP394145,PRJNA872137,The Translation Initiation Factor Homolog  eif4e1c  Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.,GSE211793,Other,The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability  yet other related families exist and are all utilized in specific contexts or tissues. Here  we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates  and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein  suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes  while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos  its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.,,pubmed:37306388,,zebrafish  RNA seq  Eif4e1c  /   rep 2 [mR2],GSM6502520,,source name:heart|tissue:heart|cell line:Mutant|genotype:Eif4e1c  / ,zebrafish  RNA seq  Eif4e1c  /   rep 2 [mR2],Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035.  This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules  TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC  2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0  based on the expressed raw reads. Assembly: GRCz11/danRer11,heart,,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.,tissue:heart|cell line:Mutant|genotype:Eif4e1c  / ,GSM6502520,GSM6502520: zebrafish  RNA seq  Eif4e1c  /   rep 2 [mR2]; Danio rerio; RNA Seq,GSM6502520 r1,GSM6502520,1,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 550,,SRP394145,,loader:fastq load.py,S4_mR2.fastq.gz,fastq,9679208152.0,127358002.0,GSM6502520 r1,0:76,A:2305039081;C:2189721629;G:2319593026;T:2864406960;N:447456,76,,,,2305039081,2189721629,2319593026,2864406960,447456,SRX17229108,SRS14795574,SRA1485233,"Biological Chemistry and Pharmacology, The Ohio State University","Biological Chemistry and Pharmacology, The Ohio State University",1,0.87011,,0.13344,,0.83633,,0.75067,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-08-22,Undetermined,Multi-stage,Heart,Cardiovascular System
71061,SRR21218376,SRX17229107,SRS14795573,SRP394145,PRJNA872137,The Translation Initiation Factor Homolog  eif4e1c  Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.,GSE211793,Other,The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability  yet other related families exist and are all utilized in specific contexts or tissues. Here  we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates  and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein  suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes  while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos  its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.,,pubmed:37306388,,zebrafish  RNA seq  Eif4e1c  /   rep 1 [mR1],GSM6502519,,source name:heart|tissue:heart|cell line:Mutant|genotype:Eif4e1c  / ,zebrafish  RNA seq  Eif4e1c  /   rep 1 [mR1],Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035.  This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules  TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC  2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0  based on the expressed raw reads. Assembly: GRCz11/danRer11,heart,,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.,tissue:heart|cell line:Mutant|genotype:Eif4e1c  / ,GSM6502519,GSM6502519: zebrafish  RNA seq  Eif4e1c  /   rep 1 [mR1]; Danio rerio; RNA Seq,GSM6502519 r1,GSM6502519,1,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 550,,SRP394145,,loader:fastq load.py,S3_mR1.fastq.gz,fastq,8635315776.0,113622576.0,GSM6502519 r1,0:76,A:2023184655;C:2026020026;G:2308108912;T:2277600404;N:401779,76,,,,2023184655,2026020026,2308108912,2277600404,401779,SRX17229107,SRS14795573,SRA1485233,"Biological Chemistry and Pharmacology, The Ohio State University","Biological Chemistry and Pharmacology, The Ohio State University",1,0.76878,,0.11592,,0.88154,,0.77541,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-08-22,Undetermined,Multi-stage,Heart,Cardiovascular System
71062,SRR21218372,SRX17229106,SRS14795572,SRP394145,PRJNA872137,The Translation Initiation Factor Homolog  eif4e1c  Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.,GSE211793,Other,The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability  yet other related families exist and are all utilized in specific contexts or tissues. Here  we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates  and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein  suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes  while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos  its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.,,pubmed:37306388,,zebrafish  RNA seq  Eif4e1c +/+  rep 2 [pR2],GSM6502518,,source name:heart|tissue:heart|cell line:Wt|genotype:Eif4e1c +/+,zebrafish  RNA seq  Eif4e1c +/+  rep 2 [pR2],Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035.  This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules  TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC  2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0  based on the expressed raw reads. Assembly: GRCz11/danRer11,heart,,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.,tissue:heart|cell line:Wt|genotype:Eif4e1c +/+,GSM6502518,GSM6502518: zebrafish  RNA seq  Eif4e1c +/+  rep 2 [pR2]; Danio rerio; RNA Seq,GSM6502518 r1,GSM6502518,1,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 550,,SRP394145,,loader:fastq load.py,S2_pR2.fastq.gz,fastq,10448850044.0,137484869.0,GSM6502518 r1,0:76,A:2430513193;C:2444194607;G:2524422424;T:3049237563;N:482257,76,,,,2430513193,2444194607,2524422424,3049237563,482257,SRX17229106,SRS14795572,SRA1485233,"Biological Chemistry and Pharmacology, The Ohio State University","Biological Chemistry and Pharmacology, The Ohio State University",1,0.8635,,0.13877,,0.8379,,0.73623,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-08-22,Undetermined,Multi-stage,Heart,Cardiovascular System
71063,SRR21218375,SRX17229105,SRS14795571,SRP394145,PRJNA872137,The Translation Initiation Factor Homolog  eif4e1c  Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.,GSE211793,Other,The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability  yet other related families exist and are all utilized in specific contexts or tissues. Here  we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates  and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein  suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes  while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos  its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.,,pubmed:37306388,,zebrafish  RNA seq  Eif4e1c +/+  rep 1 [pR1],GSM6502517,,source name:heart|tissue:heart|cell line:Wt|genotype:Eif4e1c +/+,zebrafish  RNA seq  Eif4e1c +/+  rep 1 [pR1],Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035.  This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules  TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC  2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0  based on the expressed raw reads. Assembly: GRCz11/danRer11,heart,,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.,tissue:heart|cell line:Wt|genotype:Eif4e1c +/+,GSM6502517,GSM6502517: zebrafish  RNA seq  Eif4e1c +/+  rep 1 [pR1]; Danio rerio; RNA Seq,GSM6502517 r1,GSM6502517,1,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ILLUMINA,NextSeq 550,,SRP394145,,loader:fastq load.py,S1_pR1.fastq.gz,fastq,9043049240.0,118987490.0,GSM6502517 r1,0:76,A:2135845081;C:2176730805;G:2319372876;T:2410684299;N:416179,76,,,,2135845081,2176730805,2319372876,2410684299,416179,SRX17229105,SRS14795571,SRA1485233,"Biological Chemistry and Pharmacology, The Ohio State University","Biological Chemistry and Pharmacology, The Ohio State University",1,0.80924,,0.17191,,0.84889,,0.75115,,76,,B,,usable mapping rate,illumina,nextseq,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2022-08-22,Undetermined,Multi-stage,Heart,Cardiovascular System
71064,SRR21218373,SRX17229104,SRS14795570,SRP394145,PRJNA872137,The Translation Initiation Factor Homolog  eif4e1c  Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.,GSE211793,Other,The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability  yet other related families exist and are all utilized in specific contexts or tissues. Here  we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates  and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein  suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes  while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos  its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.,,pubmed:37306388,,zebrafish  Ribo seq  Eif4e1c  /  rep2 [r mR2],GSM6502516,,source name:heart|tissue:heart|cell line:Mutant|genotype:Eif4e1c  / ,zebrafish  Ribo seq  Eif4e1c  /  rep2 [r mR2],Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035.  This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules  TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC  2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0  based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq,heart,,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.,tissue:heart|cell line:Mutant|genotype:Eif4e1c  / ,GSM6502516,GSM6502516: zebrafish  Ribo seq  Eif4e1c  /  rep2 [r mR2]; Danio rerio; OTHER,GSM6502516 r1,GSM6502516,1,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,NextSeq 550,,SRP394145,,,rS4_mR2.fastq.gz,fastq,6611131472.0,86988572.0,GSM6502516 r1,0:76 1:0,A:1748359123;C:1658689534;G:1706027528;T:1497702781;N:352506,76,0,,,1748359123,1658689534,1706027528,1497702781,352506,SRX17229104,SRS14795570,SRA1485233,"Biological Chemistry and Pharmacology, The Ohio State University","Biological Chemistry and Pharmacology, The Ohio State University",1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2022-08-22,Undetermined,Multi-stage,Heart,Cardiovascular System
71065,SRR21218374,SRX17229103,SRS14795569,SRP394145,PRJNA872137,The Translation Initiation Factor Homolog  eif4e1c  Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.,GSE211793,Other,The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability  yet other related families exist and are all utilized in specific contexts or tissues. Here  we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates  and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein  suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes  while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos  its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.,,pubmed:37306388,,zebrafish  Ribo seq  Eif4e1c  /   rep 1 [r mR1],GSM6502515,,source name:heart|tissue:heart|cell line:Mutant|genotype:Eif4e1c  / ,zebrafish  Ribo seq  Eif4e1c  /   rep 1 [r mR1],Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035.  This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules  TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC  2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0  based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq,heart,,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.,tissue:heart|cell line:Mutant|genotype:Eif4e1c  / ,GSM6502515,GSM6502515: zebrafish  Ribo seq  Eif4e1c  /   rep 1 [r mR1]; Danio rerio; OTHER,GSM6502515 r1,GSM6502515,1,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,NextSeq 550,,SRP394145,,,rS3_mR1.fastq.gz,fastq,13677356644.0,179965219.0,GSM6502515 r1,0:76 1:0,A:3346749848;C:3412648254;G:3629003006;T:3288222747;N:732789,76,0,,,3346749848,3412648254,3629003006,3288222747,732789,SRX17229103,SRS14795569,SRA1485233,"Biological Chemistry and Pharmacology, The Ohio State University","Biological Chemistry and Pharmacology, The Ohio State University",1,0.0,,0.0,,1.0,,,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2022-08-22,Undetermined,Multi-stage,Heart,Cardiovascular System
71066,SRR21218377,SRX17229102,SRS14795568,SRP394145,PRJNA872137,The Translation Initiation Factor Homolog  eif4e1c  Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.,GSE211793,Other,The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability  yet other related families exist and are all utilized in specific contexts or tissues. Here  we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates  and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein  suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes  while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos  its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.,,pubmed:37306388,,zebrafish  Ribo seq  Eif4e1c +/+  rep 2 [r pR2],GSM6502514,,source name:heart|tissue:heart|cell line:Wt|genotype:Eif4e1c +/+,zebrafish  Ribo seq  Eif4e1c +/+  rep 2 [r pR2],Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035.  This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules  TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC  2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0  based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq,heart,,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.,tissue:heart|cell line:Wt|genotype:Eif4e1c +/+,GSM6502514,GSM6502514: zebrafish  Ribo seq  Eif4e1c +/+  rep 2 [r pR2]; Danio rerio; OTHER,GSM6502514 r1,GSM6502514,1,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,NextSeq 550,,SRP394145,,,rS2_pR2.fastq.gz,fastq,8919983048.0,117368198.0,GSM6502514 r1,0:76 1:0,A:2208663451;C:2257902067;G:2371468879;T:2081476473;N:472178,76,0,,,2208663451,2257902067,2371468879,2081476473,472178,SRX17229102,SRS14795568,SRA1485233,"Biological Chemistry and Pharmacology, The Ohio State University","Biological Chemistry and Pharmacology, The Ohio State University",1,1e-05,,0.0,,0.99997,,1.0,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2022-08-22,Undetermined,Multi-stage,Heart,Cardiovascular System
71067,SRR21218378,SRX17229101,SRS14795567,SRP394145,PRJNA872137,The Translation Initiation Factor Homolog  eif4e1c  Regulates Cardiomyocyte Metabolism and Proliferation During Heart Regeneration.,GSE211793,Other,The?eIF4E family of translation initiation factors bind five prime methylated caps and act as the limiting step for mRNA translation. The canonical eIF4E1A is required for cell viability  yet other related families exist and are all utilized in specific contexts or tissues. Here  we describe a new family called Eif4e1c that is ancestral to the canonical eIF4E1A in vertebrates  and for which we find roles during heart development and regeneration in zebrafish.?The Eif4e1c family is present in all aquatic vertebrates but has been lost in all terrestrial species. A core group of amino acids shared over 500 million yrs of evolution from?ray finned fish to sharks?forms an evolutionarily conserved binding interface along the surface of the protein  suggesting Eif4e1c functions in a novel pathway.? Deletion of eif4e1c?in zebrafish caused growth deficits and impaired survival in juveniles.?Mutants surviving to maturity had fewer cardiomyocytes  while also showing reduced proliferative responses to cardiac injury. Ribosome profiling of mutant hearts demonstrated changes in translation efficiency of mRNA for genes known to regulate cardiomyocyte proliferation. Although?eif4e1c?is expressed in many tissues and is the predominant cap binding initiation homolog in embryos  its disruption had most notable impact on the heart and at juvenile stages. ?Our findings reveal context dependent requirements for translation initiation regulators during heart regeneration. Overall design: Ribosome profiling of adult uninjured eif4e1c zebrafish mutant hearts and adult uninjured EK zebrafish wildtype hearts.,,pubmed:37306388,,zebrafish  Ribo seq  Eif4e1c +/+  rep 1 [r pR1],GSM6502513,,source name:heart|tissue:heart|cell line:Wt|genotype:Eif4e1c +/+,zebrafish  Ribo seq  Eif4e1c +/+  rep 1 [r pR1],Fastq files were processed using FastQC v0.11.8; RRID:SCR 014583 for quality control QC analysis. Pre processing of sequencing reads was based on the QC report using the FASTQ Quality Filter module in the FASTX Toolkit RRID:SCR 019035.  This was used to filter the bases with 99% accuracy based on Q Score. Reads were removed that showed less than 70% of nucleotides with an accuracy of at least 99%. The sequences were collapsed according to their by Unique Molecular Identifiers UMIs. Cutadapt RRID:SCR 011841 was used to trim 21 nt adaptor before the first nt and the last 4 nt from the reads to remove the UMI. The processed reads were aligned to GRCz11/danRer11 assembly of the zebrafish genome; Genome Reference Consortium using STAR v2.5.3a RRID:SCR 004463. Generated bam files were processed with RiboProfiling package v1.2.2. Coverage counts on the coding regions CDS were obtained for each sample based on RiboProfiling function modules  TxDb.Drerio.UCSC.danRer11.refGene v3.4.6; Annotation package for TxDb objects; Team BC  2019 and GenomicFeatures package v1.46.1. Differential expression analysis was performed using the DESeq2 pipeline version 1.26.0  based on the expressed raw reads. Assembly: GRCz11/danRer11 Library strategy: Ribo seq,heart,,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer’s instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,Zebrafish used for ribosome profiling were grown together under normal conditions and were genotyped upon reaching maturity.,tissue:heart|cell line:Wt|genotype:Eif4e1c +/+,GSM6502513,GSM6502513: zebrafish  Ribo seq  Eif4e1c +/+  rep 1 [r pR1]; Danio rerio; OTHER,GSM6502513 r1,GSM6502513,1,The hearts were lysed on ice with 100ul of lysis buffer with 53 mg/ml cycloheximide using mechanical homogenization with a pestle for thirty seconds. Cells were lysed further by trituration of the sample using a 27.5 gauge needle syringe 20x on ice. Cell extracts average OD 7 were treated with MNase NEB  CaCl2 5mM final concentration  and Turbo DNAse I Invitrogen at 25°C for 30 minutes. MNase digestion was stopped with SUPERase inhibitor incubation on ice. 80S ribosomes were isolated using SH400 spin columns Cytiva. Columns were prepared according to the manufacturer's instructions. 100 µls of MNase treated sample was loaded per column and centrifuged for 2 min at 600 RCF. The flow through was isolated and incubated for 5 min. with 3x volume of Trizol LS Ambion. 200 µl of chloroform was added and incubated for 2 min. Samples were centrifuged for 15 min. at 12 000 rpm 4°C. The aqueous phase was extracted and precipitated overnight at  20°C using glycoblue ThermoFisher and isopropanol followed by centrifugation for 30 minutes at 4C at 10 000 RPM. Pellets were washed with 75% Ethanol and resuspended into RNase free water. Next Flex smRNA seq kit v3,,OTHER,TRANSCRIPTOMIC,other,SINGLE,ILLUMINA,NextSeq 550,,SRP394145,,,rS1_pR1.fastq.gz,fastq,8551941876.0,112525551.0,GSM6502513 r1,0:76 1:0,A:2015417703;C:2191682962;G:2364697448;T:1979683824;N:459939,76,0,,,2015417703,2191682962,2364697448,1979683824,459939,SRX17229101,SRS14795567,SRA1485233,"Biological Chemistry and Pharmacology, The Ohio State University","Biological Chemistry and Pharmacology, The Ohio State University",1,1e-05,,0.0,,0.99997,,0.0,,76,,T,,under 1.2% mapping rate,illumina,nextseq,unknown,other,unknown,bulk,unknown,unknown,,United States,2022-08-22,Undetermined,Multi-stage,Heart,Cardiovascular System
72819,SRR23190058,SRX19140398,SRS16550346,SRP418629,PRJNA926357,Single cell transcriptional profiles of endothelial cells  sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq],GSE223461,Transcriptome Analysis,To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development  we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts  respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization  a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs  we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO  respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,EC  MTZ  scRNAseq,GSM6956592,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:MTZ,EC  MTZ  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 5 mM MTZ  dissolved in fish water for 12 h in the dark. post exposure to chemicals  the water was changed to remove the chemicals  and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:MTZ,GSM6956592,GSM6956592: EC  MTZ  scRNAseq; Danio rerio; RNA Seq,GSM6956592 r1,GSM6956592,1,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP418629,,loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=M S1 L001 R1 001.fastq.gz   read2PairFiles=M S1 L001 R2 001.fastq.gz   read3PairFiles=M S1 L001 I1 001.fastq.gz   read4PairFiles=M S1 L001 I2 001.fastq.gz,M_S1_L001_I1_001.fastq.gz M_S1_L001_I2_001.fastq.gz M_S1_L001_R1_001.fastq.gz M_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,10297935498.0,74622721.0,GSM6956592 r1,0:28 1:90 2:10 3:10,A:2422395373;C:2014936837;G:2115011813;T:2251686635;N:1450420,28,90,10,10,2422395373,2014936837,2115011813,2251686635,1450420,SRX19140398,SRS16550346,SRA1578143,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",2,0.01687,0.92938,0.00583,0.17709,0.98549,0.82603,0.28254,0.55599,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2023-01-22,Multi-stage,Multi-stage,Heart,Cardiovascular System
72820,SRR23190059,SRX19140398,SRS16550346,SRP418629,PRJNA926357,Single cell transcriptional profiles of endothelial cells  sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq],GSE223461,Transcriptome Analysis,To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development  we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts  respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization  a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs  we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO  respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,EC  MTZ  scRNAseq,GSM6956592,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:MTZ,EC  MTZ  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 5 mM MTZ  dissolved in fish water for 12 h in the dark. post exposure to chemicals  the water was changed to remove the chemicals  and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:MTZ,GSM6956592,GSM6956592: EC  MTZ  scRNAseq; Danio rerio; RNA Seq,GSM6956592 r1,GSM6956592,1,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP418629,,loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=M S1 L002 R1 001.fastq.gz   read2PairFiles=M S1 L002 R2 001.fastq.gz   read3PairFiles=M S1 L002 I1 001.fastq.gz   read4PairFiles=M S1 L002 I2 001.fastq.gz,M_S1_L002_I1_001.fastq.gz M_S1_L002_I2_001.fastq.gz M_S1_L002_R1_001.fastq.gz M_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10255307022.0,74313819.0,GSM6956592 r2,0:28 1:90 2:10 3:10,A:2413672015;C:2007739816;G:2105898639;T:2240007297;N:1712875,28,90,10,10,2413672015,2007739816,2105898639,2240007297,1712875,SRX19140398,SRS16550346,SRA1578143,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",2,0.01711,0.93111,0.00583,0.17637,0.98514,0.82639,0.27373,0.56532,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2023-01-22,Multi-stage,Multi-stage,Heart,Cardiovascular System
72821,SRR23190060,SRX19140398,SRS16550346,SRP418629,PRJNA926357,Single cell transcriptional profiles of endothelial cells  sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq],GSE223461,Transcriptome Analysis,To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development  we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts  respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization  a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs  we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO  respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,EC  MTZ  scRNAseq,GSM6956592,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:MTZ,EC  MTZ  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 5 mM MTZ  dissolved in fish water for 12 h in the dark. post exposure to chemicals  the water was changed to remove the chemicals  and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:MTZ,GSM6956592,GSM6956592: EC  MTZ  scRNAseq; Danio rerio; RNA Seq,GSM6956592 r1,GSM6956592,1,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP418629,,loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=M S1 L003 R1 001.fastq.gz   read2PairFiles=M S1 L003 R2 001.fastq.gz   read3PairFiles=M S1 L003 I1 001.fastq.gz   read4PairFiles=M S1 L003 I2 001.fastq.gz,M_S1_L003_I1_001.fastq.gz M_S1_L003_I2_001.fastq.gz M_S1_L003_R1_001.fastq.gz M_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,10416242898.0,75480021.0,GSM6956592 r3,0:28 1:90 2:10 3:10,A:2449287942;C:2038757909;G:2142133631;T:2275795705;N:667291,28,90,10,10,2449287942,2038757909,2142133631,2275795705,667291,SRX19140398,SRS16550346,SRA1578143,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",2,0.01658,0.92887,0.00568,0.17653,0.98593,0.82795,0.28335,0.55226,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2023-01-22,Multi-stage,Multi-stage,Heart,Cardiovascular System
72822,SRR23190061,SRX19140398,SRS16550346,SRP418629,PRJNA926357,Single cell transcriptional profiles of endothelial cells  sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq],GSE223461,Transcriptome Analysis,To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development  we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts  respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization  a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs  we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO  respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,EC  MTZ  scRNAseq,GSM6956592,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:MTZ,EC  MTZ  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 5 mM MTZ  dissolved in fish water for 12 h in the dark. post exposure to chemicals  the water was changed to remove the chemicals  and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:MTZ,GSM6956592,GSM6956592: EC  MTZ  scRNAseq; Danio rerio; RNA Seq,GSM6956592 r1,GSM6956592,1,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP418629,,loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=M S1 L004 R1 001.fastq.gz   read2PairFiles=M S1 L004 R2 001.fastq.gz   read3PairFiles=M S1 L004 I1 001.fastq.gz   read4PairFiles=M S1 L004 I2 001.fastq.gz,M_S1_L004_I1_001.fastq.gz M_S1_L004_I2_001.fastq.gz M_S1_L004_R1_001.fastq.gz M_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,10441110360.0,75660220.0,GSM6956592 r4,0:28 1:90 2:10 3:10,A:2455796397;C:2044932269;G:2145932306;T:2280585820;N:659168,28,90,10,10,2455796397,2044932269,2145932306,2280585820,659168,SRX19140398,SRS16550346,SRA1578143,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",2,0.01734,0.92942,0.00594,0.17578,0.98502,0.82605,0.27199,0.55089,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2023-01-22,Multi-stage,Multi-stage,Heart,Cardiovascular System
72823,SRR23190062,SRX19140397,SRS16550345,SRP418629,PRJNA926357,Single cell transcriptional profiles of endothelial cells  sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq],GSE223461,Transcriptome Analysis,To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development  we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts  respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization  a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs  we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO  respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,EC  DMSO  scRNAseq,GSM6956591,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:DMSO,EC  DMSO  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 5 mM MTZ  dissolved in fish water for 12 h in the dark. post exposure to chemicals  the water was changed to remove the chemicals  and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:DMSO,GSM6956591,GSM6956591: EC  DMSO  scRNAseq; Danio rerio; RNA Seq,GSM6956591 r1,GSM6956591,1,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP418629,,loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=D S1 L001 R1 001.fastq.gz   read2PairFiles=D S1 L001 R2 001.fastq.gz   read3PairFiles=D S1 L001 I1 001.fastq.gz   read4PairFiles=D S1 L001 I2 001.fastq.gz,D_S1_L001_I1_001.fastq.gz D_S1_L001_I2_001.fastq.gz D_S1_L001_R1_001.fastq.gz D_S1_L001_R2_001.fastq.gz,fastq fastq fastq fastq,10595595012.0,76779674.0,GSM6956591 r1,0:28 1:90 2:10 3:10,A:2544857509;C:2041473878;G:2166945643;T:2305102603;N:1621899,28,90,10,10,2544857509,2041473878,2166945643,2305102603,1621899,SRX19140397,SRS16550345,SRA1578143,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",2,0.01657,0.92608,0.00601,0.18008,0.98602,0.82844,0.27705,0.55772,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2023-01-22,Multi-stage,Multi-stage,Heart,Cardiovascular System
72824,SRR23190063,SRX19140397,SRS16550345,SRP418629,PRJNA926357,Single cell transcriptional profiles of endothelial cells  sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq],GSE223461,Transcriptome Analysis,To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development  we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts  respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization  a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs  we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO  respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,EC  DMSO  scRNAseq,GSM6956591,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:DMSO,EC  DMSO  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 5 mM MTZ  dissolved in fish water for 12 h in the dark. post exposure to chemicals  the water was changed to remove the chemicals  and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:DMSO,GSM6956591,GSM6956591: EC  DMSO  scRNAseq; Danio rerio; RNA Seq,GSM6956591 r1,GSM6956591,1,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP418629,,loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=D S1 L002 R1 001.fastq.gz   read2PairFiles=D S1 L002 R2 001.fastq.gz   read3PairFiles=D S1 L002 I1 001.fastq.gz   read4PairFiles=D S1 L002 I2 001.fastq.gz,D_S1_L002_I1_001.fastq.gz D_S1_L002_I2_001.fastq.gz D_S1_L002_R1_001.fastq.gz D_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,10505133804.0,76124158.0,GSM6956591 r2,0:28 1:90 2:10 3:10,A:2524419025;C:2024371965;G:2148601948;T:2283479741;N:1777965,28,90,10,10,2524419025,2024371965,2148601948,2283479741,1777965,SRX19140397,SRS16550345,SRA1578143,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",2,0.01639,0.92559,0.00547,0.17815,0.98524,0.83004,0.2875,0.56427,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2023-01-22,Multi-stage,Multi-stage,Heart,Cardiovascular System
72825,SRR23190064,SRX19140397,SRS16550345,SRP418629,PRJNA926357,Single cell transcriptional profiles of endothelial cells  sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq],GSE223461,Transcriptome Analysis,To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development  we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts  respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization  a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs  we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO  respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,EC  DMSO  scRNAseq,GSM6956591,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:DMSO,EC  DMSO  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 5 mM MTZ  dissolved in fish water for 12 h in the dark. post exposure to chemicals  the water was changed to remove the chemicals  and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:DMSO,GSM6956591,GSM6956591: EC  DMSO  scRNAseq; Danio rerio; RNA Seq,GSM6956591 r1,GSM6956591,1,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP418629,,loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=D S1 L003 R1 001.fastq.gz   read2PairFiles=D S1 L003 R2 001.fastq.gz   read3PairFiles=D S1 L003 I1 001.fastq.gz   read4PairFiles=D S1 L003 I2 001.fastq.gz,D_S1_L003_I1_001.fastq.gz D_S1_L003_I2_001.fastq.gz D_S1_L003_R1_001.fastq.gz D_S1_L003_R2_001.fastq.gz,fastq fastq fastq fastq,10715702622.0,77650019.0,GSM6956591 r3,0:28 1:90 2:10 3:10,A:2573807593;C:2065042721;G:2193827962;T:2329228642;N:795324,28,90,10,10,2573807593,2065042721,2193827962,2329228642,795324,SRX19140397,SRS16550345,SRA1578143,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",2,0.0164,0.92651,0.00558,0.17924,0.98559,0.82816,0.27685,0.56637,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2023-01-22,Multi-stage,Multi-stage,Heart,Cardiovascular System
72826,SRR23190065,SRX19140397,SRS16550345,SRP418629,PRJNA926357,Single cell transcriptional profiles of endothelial cells  sorted from the hearts with ablation of Wnt/beta catenin signaling activating cardiomyocytes and without xxx [scRNA seq],GSE223461,Transcriptome Analysis,To understand how Wnt/ß catenin signaling activated cardiomyocytes ß cat ON CMs promote coronary vessel development  we performed single cell RNA sequencing of endothelial cells ECs sorted from the hearts ablated ß cat ON CMs and those from control hearts  respectively. Our analyses indicated that ß cat ON CMs regulates coronary vessel development by promoting arterialization  a step in the transition of endocardial ECs to coronary ECs. Overall design: To induce nitroreductase metronidazole NTR MTZ dependent ablation of ß cat ON CMs  we treated 5 mM MTZ or DMSO to Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF?C;5xUAS:NTR mCherry fish every other day for 4 weeks from 1 mpf. We isolated live GFP+ cells by FACS sorting from the fish treated MTZ or DMSO  respectively. Barcoded single cell cDNA libraries were prepared using the Chromium Next GEM single cell three primereagent kits v3.1 and sequenced using Illumina NextSeq 500.,parent bioproject:PRJNA926354,pubmed:39395410,,EC  DMSO  scRNAseq,GSM6956591,,source name:Heart|tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:DMSO,EC  DMSO  scRNAseq,The 10x Genomics Cell Ranger pipeline v6.1.1 was used to perform sample demultiplexing  alignment to the reference genome Danio rerio GRCz11  barcode/UMI processing  and gene counting for each cell. Assembly: GRCz11 Supplementary files format and content: tsv files contain lists of genes and barcodes for each sample  mtx files count gene UMI couns for each sample,Heart,Fish were treated with DMSO or 5 mM MTZ  dissolved in fish water for 12 h in the dark. post exposure to chemicals  the water was changed to remove the chemicals  and the fish were kept in the tank without xxx circulation. Chemicals were treated every other day.,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell 3’reagent kits v3.1 10X Genomics  1000128  according to the manufacturer’s protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,tissue:Heart|genotype:Tgfli1:EGFP;Tgcryaa:EGFP  myl7:GAL4db TCF{delta}C;5xUAS:NTR mCherry|cell type:Endothelial cells|treatment:DMSO,GSM6956591,GSM6956591: EC  DMSO  scRNAseq; Danio rerio; RNA Seq,GSM6956591 r1,GSM6956591,1,Hearts were resected from Tgfli1:EGFP;Tgmyl7:GAL4db TCFΔC;5xUAS:NTR mCherry fish treated DMSO or 5 mM MTZ for 4 weeks from 1 mpf. The resected hearts were collected into a 35 mm dish containing HBSS without xxx and magnesium. Hearts were torn and were transferred into a 12 well plate. The hearts were digested with 3 mg/ml collagenase type IV Worthington  LS004188/HBSS for 30 min at 28.5 ºC. post pipetting  the cells were collected into low binding tubes  pelleted 3000 rpm  5 min at 4ºC  and washed in 0.5% FBS/DMEM phenol red free. The cells were resuspended in 0.5% FBS/DMEM containing SYTOX blue dead cell stain Thermofisher Scientific  S34857 and sorted by a FACSFusion cell sorter BD Bioscience. Sorted cells were collected in 1% FBS/DMEM and counted by a cell counter Thermofisher scientific. The resulting endothelial cellular suspension was loaded on a 10X Chromium Controller 10X Genomics. The scRNA seq library was prepared using Chromium Next GEM single cell three primereagent kits v3.1 10X Genomics  1000128  according to the manufacturer's protocol. Following droplet generation and barcoding  cDNA was synthesized and amplified. The cDNA was processed to construct Illumine sequencing libraries. Sequencing was performed on a NextSeq 500 Illumina. Raw sequencing data were processed using 10X Genomics Cell Ranger software v6.1.1.,,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,cDNA,PAIRED,ILLUMINA,NextSeq 500,,SRP418629,,loader:fastq load.py|options:  readTypes=BBTT   read1PairFiles=D S1 L004 R1 001.fastq.gz   read2PairFiles=D S1 L004 R2 001.fastq.gz   read3PairFiles=D S1 L004 I1 001.fastq.gz   read4PairFiles=D S1 L004 I2 001.fastq.gz,D_S1_L004_I1_001.fastq.gz D_S1_L004_I2_001.fastq.gz D_S1_L004_R1_001.fastq.gz D_S1_L004_R2_001.fastq.gz,fastq fastq fastq fastq,10731126882.0,77761789.0,GSM6956591 r4,0:28 1:90 2:10 3:10,A:2577638514;C:2068754148;G:2196571470;T:2332228096;N:698874,28,90,10,10,2577638514,2068754148,2196571470,2332228096,698874,SRX19140397,SRS16550345,SRA1578143,"Department of Pharmacology, Yamagata University","Department of Pharmacology, Yamagata University",2,0.01687,0.9273,0.00577,0.18031,0.98476,0.82954,0.28103,0.55337,28,90,T,B,sc-like readlen,illumina,nextseq,unknown,cdna_unspecified,unknown,sc,single_cell_droplet,10x,,Japan,2023-01-22,Multi-stage,Multi-stage,Heart,Cardiovascular System