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 10216,ERR6501834,ERX6129007,ERS7415871,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Uninjured 3,SAMEA9691614,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691614|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 6 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 3|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Uninjured 3 p,Uninjured 3 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,un-3_R1_001.fastq.gz un-3_R2_001.fastq.gz,fastq fastq,18723567013.0,65061888.0,E MTAB 10860:un 3 R,0:143.87 1:143.91,A:4417527025;C:4932613578;G:4960694819;T:4412305366;N:426225,143,143,,,4417527025,4932613578,4960694819,4412305366,426225,ERX6129007,ERS7415871,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.96755,0.96744,0.18873,0.18936,0.72868,0.73235,0.632,0.6437,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System 10217,ERR6501833,ERX6129006,ERS7415870,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Uninjured 2,SAMEA9691613,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691613|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 5 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 2|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Uninjured 2 p,Uninjured 2 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,un-2_R1_001.fastq.gz un-2_R2_001.fastq.gz,fastq fastq,16871358399.0,59064661.0,E MTAB 10860:un 2 R,0:142.77 1:142.88,A:4041490134;C:4380856328;G:4414614946;T:4033723935;N:673056,142,142,,,4041490134,4380856328,4414614946,4033723935,673056,ERX6129006,ERS7415870,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.96589,0.9656,0.15519,0.15447,0.70887,0.71062,0.60267,0.60735,150,147,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System 10218,ERR6501832,ERX6129005,ERS7415869,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Uninjured 1,SAMEA9691612,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691612|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Uninjured 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 4 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Uninjured 1|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Uninjured 1 p,Uninjured 1 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:n1,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,un-1_R1_001.fastq.gz un-1_R2_001.fastq.gz,fastq fastq,22029484310.0,76938931.0,E MTAB 10860:un 1 R,0:143.11 1:143.22,A:5407867825;C:5589867496;G:5636111894;T:5394805343;N:831752,143,143,,,5407867825,5589867496,5636111894,5394805343,831752,ERX6129005,ERS7415869,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.9602,0.95957,0.14282,0.14408,0.69649,0.69954,0.56712,0.56916,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System 10219,ERR6501831,ERX6129004,ERS7415868,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Injured 3,SAMEA9691611,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691611|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 3|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 3 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 3|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Injured 3 p,Injured 3 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:laser injury,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,in-3_R1_001.fastq.gz in-3_R2_001.fastq.gz,fastq fastq,7393087749.0,25640713.0,E MTAB 10860:in 3 R,0:144.14 1:144.20,A:1776335117;C:1913125420;G:1928181998;T:1775255039;N:190175,144,144,,,1776335117,1913125420,1928181998,1775255039,190175,ERX6129004,ERS7415868,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.96032,0.96001,0.15921,0.15882,0.71417,0.71869,0.59876,0.595,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System 10220,ERR6501830,ERX6129003,ERS7415867,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Injured 2,SAMEA9691610,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691610|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 2|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 2 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 2|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Injured 2 p,Injured 2 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:laser injury,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,in-2_R1_001.fastq.gz in-2_R2_001.fastq.gz,fastq fastq,9437508186.0,33059234.0,E MTAB 10860:in 2 R,0:142.70 1:142.77,A:2291798254;C:2421252733;G:2436117818;T:2288107030;N:232351,142,142,,,2291798254,2421252733,2436117818,2288107030,232351,ERX6129003,ERS7415867,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.96099,0.96042,0.14616,0.14802,0.70331,0.70674,0.53288,0.54459,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System 10221,ERR6501829,ERX6129002,ERS7415866,ERP131229,PRJEB46994,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E-MTAB-10860,Transcriptome Analysis,This experiment sought to understand the transcriptomic changes that occur in the larval zebrafish heart following injury. 600 hearts were laser injured at 3 dpf extracted 48 hours later and pooled into three groups of 200. RNA was extracted from the whole hearts and sent for sequencing along with 3 groups of 200 uninjured hearts extracted and processed identically. RNA sequencing quality control and alignment was performed by the commercial company GENEWIZ.,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,,Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Injured 1,SAMEA9691609,University Of Edinburgh,ENA first public:2021 10 01|ENA last update:2021 10 01|External Id:SAMEA9691609|INSDC center alias:UOE|INSDC center name:University Of Edinburgh|INSDC first public:2021 10 01T00:25:01Z|INSDC last update:2021 10 01T00:25:01Z|INSDC status:public|Submitter Id:E MTAB 10860:Injured 1|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larval stage|genotype:wild type genotype|individual:pool 1 of 200 larvae|organism part:heart|sample name:E MTAB 10860:Injured 1|sex:not available|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,E MTAB 10860:Injured 1 p,Injured 1 p,Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. We adapted the protocol of Burns and MacRae75 to increase the yield of heart retrieval from 50% to 70%. Briefly 30 larvae were placed in 2mL eppendorf tubes the conditioned water drained and replaced with ice cold Leibovitz's L 15 Medium supplemented with 10% FCS. A 19 gauge needle coupled to a 5mL syringe was used to shear the larvae by aspiration and therefore dissociate hearts from the rest of the larva. The lysate was then inspected by epifluorescence microscopy and mRFP+ hearts and collected to be kept on ice. Hearts were then digested for 10 minutes at 4°C in protease solution 5 mM CaCl2 10 mg/ml B. Licheniformis protease 125 U/mL DNase I in 1x PBS with occasional aspiration to aid digestion. Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5°C in conditioned media/water + 0.1% methylene blue w/v + 0.003% phenylthiourea. At 48 hpi uninjured and injured larvae were given an overdose of tricaine at 400 μg/ml following which hearts were extracted. RNA was then extracted using a RNeasy Plus Micro Kit Qiagen following direct lysis with RLT lysis buffer according to manufacturer's instructions. RNA concentration was measured by Qubit and integrity by Bioanalyser. RIN score for all samples ranged between 9.6 10. cDNA libraries were prepared following the standardised protocols of Illumina Novaseq 6000 the protocol is lengthy and available at https://support.illumina.com/content/dam/illumina support/documents/documentation/system documentation/novaseq/novaseq 6000 denature dilute libraries guide 1000000106351 03.pdf,Experimental Factor: injury:laser injury,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP131229,Illumina NovaSeq 6000 paired end sequencing; Bulk RNA seq dataset of uninjured vs injured larval zebrafish hearts at 48 xxx post injury on 5 dpf,ENA FIRST PUBLIC:2021 10 01|ENA LAST UPDATE:2021 10 01,in-1_R1_001.fastq.gz in-1_R2_001.fastq.gz,fastq fastq,15465552702.0,54194727.0,E MTAB 10860:in 1 R,0:142.59 1:142.78,A:3807777989;C:3911855097;G:3946385823;T:3798685145;N:848648,142,142,,,3807777989,3911855097,3946385823,3798685145,848648,ERX6129002,ERS7415866,ERA5680505,University Of Edinburgh|European Nucleotide Archive,University Of Edinburgh|European Nucleotide Archive,2,0.95721,0.95688,0.14331,0.14374,0.70262,0.70445,0.5114,0.52855,140,140,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,bulk,bulk,,United Kingdom,2021-10-01,Larval,Larval,Heart,Cardiovascular System 11017,ERR9750937,ERX9298876,ERS12023662,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 2 Uninjured,SAMEA14418104,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418104|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 Uninjured|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 10643:Expt 2 Uninjured|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 2 Uninjured p,Expt 2 Uninjured p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:n1|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_Uninjured_S2_L002_I1_001.fastq.gz E2_Uninjured_S2_L002_I2_001.fastq.gz E2_Uninjured_S2_L002_R1_001.fastq.gz E2_Uninjured_S2_L002_R2_001.fastq.gz,fastq fastq fastq fastq,9325673775.0,69079065.0,E MTAB 10643:Expt 2 Uninjured,0:10 1:10 2:28 3:87,A:1619571910;C:1420805235;G:1471531128;T:1496998088;N:972294,10,10,28,87,1619571910,1420805235,1471531128,1496998088,972294,ERX9298876,ERS12023662,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.93798,,0.11364,,0.84843,,0.53531,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System 11018,ERR9750936,ERX9298875,ERS12023661,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 2 Sham,SAMEA14418103,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418103|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 Sham|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:sham surgery|organism part:heart|sample name:E MTAB 10643:Expt 2 Sham|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 2 Sham p,Expt 2 Sham p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:sham surgery|Experimental Factor: time:3|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_Sham_S1_L002_I1_001.fastq.gz E2_Sham_S1_L002_I2_001.fastq.gz E2_Sham_S1_L002_R1_001.fastq.gz E2_Sham_S1_L002_R2_001.fastq.gz,fastq fastq fastq fastq,11328674040.0,83916104.0,E MTAB 10643:Expt 2 Sham,0:10 1:10 2:28 3:87,A:1955327720;C:1746332187;G:1777122701;T:1820705338;N:1213102,10,10,28,87,1955327720,1746332187,1777122701,1820705338,1213102,ERX9298875,ERS12023661,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.92847,,0.09981,,0.85707,,0.46947,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System 11019,ERR9750935,ERX9298874,ERS12023660,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 2 3d post amputation,SAMEA14418102,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418102|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 2 3d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 2 3d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 2 3d post amputation p,Expt 2 3d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_3dpa_S3_L002_I1_001.fastq.gz E2_3dpa_S3_L002_I2_001.fastq.gz E2_3dpa_S3_L002_R1_001.fastq.gz E2_3dpa_S3_L002_R2_001.fastq.gz,fastq fastq fastq fastq,16111486440.0,119344344.0,E MTAB 10643:Expt 2 3d post amputation,0:10 1:10 2:28 3:87,A:2610144058;C:2617445332;G:2496763759;T:2656876552;N:1728227,10,10,28,87,2610144058,2617445332,2496763759,2656876552,1728227,ERX9298874,ERS12023660,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.94868,,0.07071,,0.89221,,0.54333,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System 11020,ERR9750934,ERX9298873,ERS12023659,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 3 3d post amputation + MMP inhibitor,SAMEA14418101,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418101|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor|sex:male|strain:AB|treatment:matrix metalloproteinase inhibitor,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor p,Expt 3 3d post amputation + MMP inhibitor p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Zebrafish were treated with MMP inhibitor NSC405020 for three days following surgery. Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:matrix metalloproteinase inhibitor,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E2_3dpa_inhibitor_S4_L002_I1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_I2_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R1_001.fastq.gz E2_3dpa_inhibitor_S4_L002_R2_001.fastq.gz,fastq fastq fastq fastq,8621019270.0,63859402.0,E MTAB 10643:Expt 3 3d post amputation + MMP inhibitor,0:10 1:10 2:28 3:87,A:1438763050;C:1365497247;G:1350808021;T:1399773154;N:926502,10,10,28,87,1438763050,1365497247,1350808021,1399773154,926502,ERX9298873,ERS12023659,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.92796,,0.08671,,0.87176,,0.55088,,87,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System 11021,ERR9750933,ERX9298872,ERS12023658,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 Uninjured,SAMEA14418100,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418100|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 Uninjured|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|organism part:heart|sample name:E MTAB 10643:Expt 1 Uninjured|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 Uninjured p,Expt 1 Uninjured p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:n1|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_Uninjured_S1_L002_I1_001.fastq.gz E1_Uninjured_S1_L002_R1_001.fastq.gz E1_Uninjured_S1_L002_R2_001.fastq.gz,fastq fastq fastq,8575585211.0,67524293.0,E MTAB 10643:Expt 1 Uninjured,0:8 1:28 2:91,A:1801503847;C:1312196506;G:1367890726;T:1663053783;N:65801,8,28,91,,1801503847,1312196506,1367890726,1663053783,65801,ERX9298872,ERS12023658,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.9169,,0.11202,,0.81576,,0.54253,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System 11022,ERR9750932,ERX9298871,ERS12023657,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 7d post amputation,SAMEA14418099,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418099|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 7d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 7d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 7d post amputation p,Expt 1 7d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:7|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_7d_S3_L002_I1_001.fastq.gz E1_7d_S3_L002_R1_001.fastq.gz E1_7d_S3_L002_R2_001.fastq.gz,fastq fastq fastq,17341796660.0,136549580.0,E MTAB 10643:Expt 1 7d post amputation,0:8 1:28 2:91,A:3506600812;C:2774617588;G:2814960106;T:3329701112;N:132162,8,28,91,,3506600812,2774617588,2814960106,3329701112,132162,ERX9298871,ERS12023657,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.90616,,0.09608,,0.82446,,0.46632,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System 11023,ERR9750931,ERX9298870,ERS12023656,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 3d post amputation,SAMEA14418098,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418098|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 3d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 3d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 3d post amputation p,Expt 1 3d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:3|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_3d_S2_L002_I1_001.fastq.gz E1_3d_S2_L002_R1_001.fastq.gz E1_3d_S2_L002_R2_001.fastq.gz,fastq fastq fastq,8183008018.0,64433134.0,E MTAB 10643:Expt 1 3d post amputation,0:8 1:28 2:91,A:1630460899;C:1330248096;G:1326144211;T:1576499358;N:62630,8,28,91,,1630460899,1330248096,1326144211,1576499358,62630,ERX9298870,ERS12023656,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.88759,,0.08679,,0.82948,,0.47863,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System 11024,ERR9750930,ERX9298869,ERS12023655,ERP137743,PRJEB52989,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E-MTAB-10643,Transcriptome Analysis,Adult zebrafish hearts have the ability to regenerate. The roles of non myocytes in this process have remained elusive. Here we have performed 2 scRNAseq experiments on interstitial cells. Experiment 1 E1 included interstitial cells obtained from uninjured regenerating 3 days 7 days and 14 days post apical amputation. Experiment 2 E2 included cells from uninjured sham operated abdomen opened and regenerating 3 dy post amputation with and without xxx inhibitor NSC40520 treatment. Cells were obtained by heart dissection followed by enzymatic dissociation and FACS sorting of single viable nucleated cells.,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,,Protocols: Zebrafish were euthanized in tricaine and hearts were extracted in PBS Hearts were pooled and pre digested for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum. The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.,Expt 1 14d post amputation,SAMEA14418097,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.",ENA first public:2022 05 20|ENA last update:2022 05 20|External Id:SAMEA14418097|INSDC center alias:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC center name:IGF CNRS INSERM Univ. Montpellier LabEx ICST F 34094 Montpellier France.|INSDC first public:2022 05 20T16:17:49Z|INSDC last update:2022 05 20T16:17:49Z|INSDC status:public|Submitter Id:E MTAB 10643:Expt 1 14d post amputation|age:6|broker name:ArrayExpress|cell type:interstitial cell|common name:zebrafish|developmental stage:adult|genotype:wild type genotype|injury:20 percent removal of the cardiac ventricle apex|organism part:heart|sample name:E MTAB 10643:Expt 1 14d post amputation|sex:male|strain:AB,,,,,,,,,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,E MTAB 10643:Expt 1 14d post amputation p,Expt 1 14d post amputation p,scRNAseq of post amputation regenerating zebrafish cardiac ventricle,"Zebrafish were euthanized in tricaine and hearts were extracted in PBS ""Hearts were pooled and """"pre digested"""" for 1h in 1/10 TrypLE/HBSS No CaMg on ice. Hearts were then digested in Collagenase IV 5mg/ml + Collagenase II 5mg/ml in HBSS with 12.5uM CaCl2 at 32 deg on a shaker 800rpm for 45 min. Following this tissue was gently dissociated and passed through a cell strainer 40um spun down 5min 300g and resuspended in HBSS 2% fetal calf serum."" The heart was exposed and approximately 20% of the ventricle removed Amplified cDNA was used for three prime RNA seq library generation RNA seq libraries were prepared following the manufacturer's user guide 10x Genomics.",Experimental Factor: injury:20 percent removal of the cardiac ventricle apex|Experimental Factor: time:14|Experimental Factor: treatment:n1,RNA-Seq,TRANSCRIPTOMIC SINGLE CELL,PolyA,SINGLE,ILLUMINA,Illumina NovaSeq 6000,,ERP137743,Illumina NovaSeq 6000 sequencing; scRNAseq of post amputation regenerating zebrafish cardiac ventricle,ENA FIRST PUBLIC:2022 05 20|ENA LAST UPDATE:2022 05 20,E1_14d_S4_L002_I1_001.fastq.gz E1_14d_S4_L002_R1_001.fastq.gz E1_14d_S4_L002_R2_001.fastq.gz,fastq fastq fastq,12911908390.0,101668570.0,E MTAB 10643:Expt 1 14d post amputation,0:8 1:28 2:91,A:2700371496;C:1971281481;G:2062280628;T:2517806408;N:99857,8,28,91,,2700371496,1971281481,2062280628,2517806408,99857,ERX9298869,ERS12023655,ERA14538536,"IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive","IGF, CNRS, INSERM, Univ. Montpellier, LabEx ICST, F-34094 Montpellier, France.|European Nucleotide Archive",1,0.90771,,0.11048,,0.81523,,0.53024,,91,,B,,usable mapping rate,illumina,novaseq_era,3prime,poly_a,unknown,sc,single_cell_droplet,10x,,France,2022-05-20,Adult,Adult,Heart,Cardiovascular System 31715,SRR28508805,SRX24109965,SRS20897113,SRP498846,PRJNA1094457,Danio rerio Transcriptome or Gene expression,PRJNA1094457,Other,Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.,,,,myh6+/ 3,Sample 6,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:myh6+/ |BioSampleModel:Model organism or animal,,,,,,,,,myh6+/ 3,Sample 6,Sample 6,Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498846,,,7_230906N_S64_L004_R1_001.fastq.gz 7_230906N_S64_L004_R2_001.fastq.gz,fastq fastq,5096818364.0,16876882.0,7 230906N S64 L004 R1 001.fastq.gz,0:151 1:151,A:1417476599;C:1123713516;G:1180970526;T:1374564888;N:92835,151,151,,,1417476599,1123713516,1180970526,1374564888,92835,SRX24109965,SRS20897113,SRA1836610,Nanjing medical university|Cardiology,Nanjing medical university,2,0.92843,0.93025,0.09825,0.0937,0.7601,0.76081,0.46245,0.45548,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-31,Adult,Adult,Heart,Cardiovascular System 31716,SRR28508806,SRX24109964,SRS20897112,SRP498846,PRJNA1094457,Danio rerio Transcriptome or Gene expression,PRJNA1094457,Other,Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.,,,,myh6+/ 2,Sample 5,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:myh6+/ |BioSampleModel:Model organism or animal,,,,,,,,,myh6+/ 2,Sample 5,Sample 5,Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498846,,,5_230906N_S62_L004_R2_001.fastq.gz 5_230906N_S62_L004_R1_001.fastq.gz,fastq fastq,6194790402.0,20512551.0,5 230906N S62 L004 R1 001.fastq.gz,0:151 1:151,A:1714858851;C:1363381540;G:1448185824;T:1668247206;N:116981,151,151,,,1714858851,1363381540,1448185824,1668247206,116981,SRX24109964,SRS20897112,SRA1836610,Nanjing medical university|Cardiology,Nanjing medical university,2,0.93019,0.93196,0.09367,0.08848,0.75444,0.75741,0.48694,0.48749,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-31,Adult,Adult,Heart,Cardiovascular System 31717,SRR28508807,SRX24109963,SRS20897111,SRP498846,PRJNA1094457,Danio rerio Transcriptome or Gene expression,PRJNA1094457,Other,Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.,,,,myh6+/ 1,Sample 4,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:myh6+/ |BioSampleModel:Model organism or animal,,,,,,,,,myh6+/ 1,Sample 4,Sample 4,Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498846,,,1_230906N_S59_L004_R2_001.fastq.gz 1_230906N_S59_L004_R1_001.fastq.gz,fastq fastq,5707073690.0,18897595.0,1 230906N S59 L004 R1 001.fastq.gz,0:151 1:151,A:1590227722;C:1248119772;G:1327453455;T:1541167866;N:104875,151,151,,,1590227722,1248119772,1327453455,1541167866,104875,SRX24109963,SRS20897111,SRA1836610,Nanjing medical university|Cardiology,Nanjing medical university,2,0.92942,0.93069,0.10355,0.09914,0.75745,0.76041,0.48155,0.48754,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-31,Adult,Adult,Heart,Cardiovascular System 31718,SRR28508808,SRX24109962,SRS20897110,SRP498846,PRJNA1094457,Danio rerio Transcriptome or Gene expression,PRJNA1094457,Other,Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.,,,,WT 3,Sample 3,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:wild type|BioSampleModel:Model organism or animal,,,,,,,,,WT 3,Sample 3,Sample 3,Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498846,,,6_230906N_S63_L004_R1_001.fastq.gz 6_230906N_S63_L004_R2_001.fastq.gz,fastq fastq,6134248160.0,20312080.0,6 230906N S63 L004 R1 001.fastq.gz,0:151 1:151,A:1703789586;C:1348484209;G:1426369972;T:1655488984;N:115409,151,151,,,1703789586,1348484209,1426369972,1655488984,115409,SRX24109962,SRS20897110,SRA1836610,Nanjing medical university|Cardiology,Nanjing medical university,2,0.92941,0.93008,0.087,0.08333,0.76946,0.77033,0.47664,0.48975,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-31,Adult,Adult,Heart,Cardiovascular System 31719,SRR28508809,SRX24109961,SRS20897109,SRP498846,PRJNA1094457,Danio rerio Transcriptome or Gene expression,PRJNA1094457,Other,Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.,,,,WT 2,Sample 2,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:wild type|BioSampleModel:Model organism or animal,,,,,,,,,WT 2,Sample 2,Sample 2,Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498846,,,4_230906N_S61_L004_R1_001.fastq.gz 4_230906N_S61_L004_R2_001.fastq.gz,fastq fastq,6573338342.0,21766021.0,4 230906N S61 L004 R1 001.fastq.gz,0:151 1:151,A:1838220811;C:1442852455;G:1512987676;T:1779153110;N:124290,151,151,,,1838220811,1442852455,1512987676,1779153110,124290,SRX24109961,SRS20897109,SRA1836610,Nanjing medical university|Cardiology,Nanjing medical university,2,0.9373,0.93754,0.08495,0.07972,0.7766,0.77897,0.48726,0.50532,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-31,Adult,Adult,Heart,Cardiovascular System 31720,SRR28508810,SRX24109960,SRS20897108,SRP498846,PRJNA1094457,Danio rerio Transcriptome or Gene expression,PRJNA1094457,Other,Atrial cardiomyopathy which often comes with underlying genetic defects has been recognized as a possible substrate of atrial fibrillation. MYH6 encodes a myosin heavy chain a MHC predominantly expressed in the atria and pivotal in sarcomere organization and muscle contraction. However the role of MYH6 in atrial diseases has not been fully elucidated and the genetic cause of atrial cardiomyopathy needs further investigation. Here we employed CRISPR/Cas9 to generate myh6 knockout zebrafish assessing cardiac function through diverse methodologies including video analysis ECG echocardiography transmission electron microscopy and transcriptomic sequencing. Our findings revealed that myh6 defects in zebrafish led to impaired atrial and ventricular function and disordered sarcomere. This research underscores the pivotal role of MYH6 in maintaining atrial function and development. The observed connections between sarcomeric gene variants and atrial cardiomyopathy contribute to our understanding of the genetic basis of atrial fibrillation.,,,,WT 1,Sample 1,,strain:not collected|isolate:not collected|breed:not collected|cultivar:not collected|ecotype:not collected|age:6 mpf|dev stage:not collected|collection date:2023 09 03|geo loc name:not collected|sex:pooled male and female|tissue:heart|genotype:wild type|BioSampleModel:Model organism or animal,,,,,,,,,WT 1,Sample 1,Sample 1,Sequencing data were analyzed by R studio Version 2023.03.0+386. Differentially expressed genes DEGs between the experimental myh6+/ and control wildtype groups were identified using the DESeq2 package.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP498846,,,3_230906N_S1_L004_R2_001.fastq.gz 3_230906N_S1_L004_R1_001.fastq.gz,fastq fastq,6962707546.0,23055323.0,3 230906N S1 L004 R1 001.fastq.gz,0:151 1:151,A:1938531865;C:1527591368;G:1608823948;T:1887630666;N:129699,151,151,,,1938531865,1527591368,1608823948,1887630666,129699,SRX24109960,SRS20897108,SRA1836610,Nanjing medical university|Cardiology,Nanjing medical university,2,0.84836,0.93866,0.08283,0.08602,0.7696,0.764,0.48014,0.48678,151,151,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2024-03-31,Adult,Adult,Heart,Cardiovascular System 52916,SRR9596460,SRX6362169,SRS5024083,SRP211964,PRJNA551130,Induction of adult cardiomyocyte renewal by Klf1,PRJNA551130,Other,In highly regenerative animals cardiac regeneration occurs innately through cardiomyocyte dedifferentiation and proliferation although the regenerative mechanisms remain unclear. This project contains raw sequencing data sets that were used to identify that klf1 a Kruppel like transcription factor essential for red blood cell development is also necessary and sufficient in the myocardium for the induction of cardiomyocyte dedifferentiation and proliferation in adult zebrafish hearts,,,klf1 over expressing,,klf1,,strain:EKW|breed:n1|cultivar:n1|ecotype:n1|dev stage:Adult|sex:pooled male and female|tissue:hearts|genotype:klf1 overexpressing|sample type:tissue sample|treatment:untreated|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish cardiac tissue,OE1 RNASEQ,OE1 RNASEQ,Tissue was resuspended in 700ul Trizol and total RNA was extracted using miRNeasy kit following manufacturers description. Total RNA integrity was assessed and quantified on a RNA nano Agilent chip following manufacturers description. RNA libraries were prepared 500ng input using the Kapa stranded RNA Seq kit using the oligo dT module to enrich for mRNA transcripts. Libraries were pooled to equimolar concentrations and sequenced on an Illumina HiSeq2500 paired end reads using v4 high output chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP211964,,,CCB6CANXX_5_180204_CFL--000_Other_ATCACG_R_180116_DAVHUM_LIB2500_M003_R1.fastq.gz CCB6CANXX_5_180204_CFL--000_Other_ATCACG_R_180116_DAVHUM_LIB2500_M003_R2.fastq.gz,fastq fastq,6046387500.0,24185550.0,CCB6CANXX 5 180204 CFL 000 Other ATCACG R 180116 DAVHUM LIB2500 M003 R1.fastq.gz,0:125 1:125,A:1668794703;C:1351121805;G:1358418631;T:1666534929;N:1517432,125,125,,,1668794703,1351121805,1358418631,1666534929,1517432,SRX6362169,SRS5024083,SRA913571,Victor Chang Cardiac Research Institute|Genome core,Victor Chang Cardiac Research Institute,2,0.93849,0.94275,0.11483,0.11515,0.73979,0.74251,0.49919,0.49697,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2019-06-26,Adult,Adult,Heart,Cardiovascular System 52917,SRR9596461,SRX6362168,SRS5024083,SRP211964,PRJNA551130,Induction of adult cardiomyocyte renewal by Klf1,PRJNA551130,Other,In highly regenerative animals cardiac regeneration occurs innately through cardiomyocyte dedifferentiation and proliferation although the regenerative mechanisms remain unclear. This project contains raw sequencing data sets that were used to identify that klf1 a Kruppel like transcription factor essential for red blood cell development is also necessary and sufficient in the myocardium for the induction of cardiomyocyte dedifferentiation and proliferation in adult zebrafish hearts,,,klf1 over expressing,,klf1,,strain:EKW|breed:n1|cultivar:n1|ecotype:n1|dev stage:Adult|sex:pooled male and female|tissue:hearts|genotype:klf1 overexpressing|sample type:tissue sample|treatment:untreated|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish cardiac tissue,OE2 RNASEQ,OE2 RNASEQ,Tissue was resuspended in 700ul Trizol and total RNA was extracted using miRNeasy kit following manufacturers description. Total RNA integrity was assessed and quantified on a RNA nano Agilent chip following manufacturers description. RNA libraries were prepared 500ng input using the Kapa stranded RNA Seq kit using the oligo dT module to enrich for mRNA transcripts. Libraries were pooled to equimolar concentrations and sequenced on an Illumina HiSeq2500 paired end reads using v4 high output chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP211964,,,CCB6CANXX_5_180204_CFL--002_Other_TTAGGC_R_180116_DAVHUM_LIB2500_M003_R1.fastq.gz CCB6CANXX_5_180204_CFL--002_Other_TTAGGC_R_180116_DAVHUM_LIB2500_M003_R2.fastq.gz,fastq fastq,6511647250.0,26046589.0,CCB6CANXX 5 180204 CFL 002 Other TTAGGC R 180116 DAVHUM LIB2500 M003 R1.fastq.gz,0:125 1:125,A:1807264422;C:1439461808;G:1458452089;T:1804785270;N:1683661,125,125,,,1807264422,1439461808,1458452089,1804785270,1683661,SRX6362168,SRS5024083,SRA913571,Victor Chang Cardiac Research Institute|Genome core,Victor Chang Cardiac Research Institute,2,0.93772,0.94197,0.11227,0.11206,0.73387,0.73689,0.55595,0.55246,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2019-06-26,Adult,Adult,Heart,Cardiovascular System 52918,SRR9596462,SRX6362167,SRS5024083,SRP211964,PRJNA551130,Induction of adult cardiomyocyte renewal by Klf1,PRJNA551130,Other,In highly regenerative animals cardiac regeneration occurs innately through cardiomyocyte dedifferentiation and proliferation although the regenerative mechanisms remain unclear. This project contains raw sequencing data sets that were used to identify that klf1 a Kruppel like transcription factor essential for red blood cell development is also necessary and sufficient in the myocardium for the induction of cardiomyocyte dedifferentiation and proliferation in adult zebrafish hearts,,,klf1 over expressing,,klf1,,strain:EKW|breed:n1|cultivar:n1|ecotype:n1|dev stage:Adult|sex:pooled male and female|tissue:hearts|genotype:klf1 overexpressing|sample type:tissue sample|treatment:untreated|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish cardiac tissue,OE3 RNASEQ,OE3 RNASEQ,Tissue was resuspended in 700ul Trizol and total RNA was extracted using miRNeasy kit following manufacturers description. Total RNA integrity was assessed and quantified on a RNA nano Agilent chip following manufacturers description. RNA libraries were prepared 500ng input using the Kapa stranded RNA Seq kit using the oligo dT module to enrich for mRNA transcripts. Libraries were pooled to equimolar concentrations and sequenced on an Illumina HiSeq2500 paired end reads using v4 high output chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP211964,,,CCB6CANXX_5_180204_CFL--006_Other_ACTTGA_R_180116_DAVHUM_LIB2500_M003_R1.fastq.gz CCB6CANXX_5_180204_CFL--006_Other_ACTTGA_R_180116_DAVHUM_LIB2500_M003_R2.fastq.gz,fastq fastq,6173169750.0,24692679.0,CCB6CANXX 5 180204 CFL 006 Other ACTTGA R 180116 DAVHUM LIB2500 M003 R1.fastq.gz,0:125 1:125,A:1706550006;C:1374108830;G:1394428093;T:1696508705;N:1574116,125,125,,,1706550006,1374108830,1394428093,1696508705,1574116,SRX6362167,SRS5024083,SRA913571,Victor Chang Cardiac Research Institute|Genome core,Victor Chang Cardiac Research Institute,2,0.93202,0.93602,0.11765,0.11618,0.732,0.73478,0.54315,0.5277,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2019-06-26,Adult,Adult,Heart,Cardiovascular System 52919,SRR9596463,SRX6362166,SRS5024083,SRP211964,PRJNA551130,Induction of adult cardiomyocyte renewal by Klf1,PRJNA551130,Other,In highly regenerative animals cardiac regeneration occurs innately through cardiomyocyte dedifferentiation and proliferation although the regenerative mechanisms remain unclear. This project contains raw sequencing data sets that were used to identify that klf1 a Kruppel like transcription factor essential for red blood cell development is also necessary and sufficient in the myocardium for the induction of cardiomyocyte dedifferentiation and proliferation in adult zebrafish hearts,,,klf1 over expressing,,klf1,,strain:EKW|breed:n1|cultivar:n1|ecotype:n1|dev stage:Adult|sex:pooled male and female|tissue:hearts|genotype:klf1 overexpressing|sample type:tissue sample|treatment:untreated|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish cardiac tissue,OE4 RNASEQ,OE4 RNASEQ,Tissue was resuspended in 700ul Trizol and total RNA was extracted using miRNeasy kit following manufacturers description. Total RNA integrity was assessed and quantified on a RNA nano Agilent chip following manufacturers description. RNA libraries were prepared 500ng input using the Kapa stranded RNA Seq kit using the oligo dT module to enrich for mRNA transcripts. Libraries were pooled to equimolar concentrations and sequenced on an Illumina HiSeq2500 paired end reads using v4 high output chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP211964,,,CCB6CANXX_5_180204_CFL--007_Other_GATCAG_R_180116_DAVHUM_LIB2500_M003_R1.fastq.gz CCB6CANXX_5_180204_CFL--007_Other_GATCAG_R_180116_DAVHUM_LIB2500_M003_R2.fastq.gz,fastq fastq,7295330500.0,29181322.0,CCB6CANXX 5 180204 CFL 007 Other GATCAG R 180116 DAVHUM LIB2500 M003 R1.fastq.gz,0:125 1:125,A:2032530437;C:1615271949;G:1627524722;T:2018148293;N:1855099,125,125,,,2032530437,1615271949,1627524722,2018148293,1855099,SRX6362166,SRS5024083,SRA913571,Victor Chang Cardiac Research Institute|Genome core,Victor Chang Cardiac Research Institute,2,0.9317,0.93743,0.11776,0.11755,0.73497,0.73888,0.51221,0.53503,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2019-06-26,Adult,Adult,Heart,Cardiovascular System 52920,SRR9596464,SRX6362165,SRS5024084,SRP211964,PRJNA551130,Induction of adult cardiomyocyte renewal by Klf1,PRJNA551130,Other,In highly regenerative animals cardiac regeneration occurs innately through cardiomyocyte dedifferentiation and proliferation although the regenerative mechanisms remain unclear. This project contains raw sequencing data sets that were used to identify that klf1 a Kruppel like transcription factor essential for red blood cell development is also necessary and sufficient in the myocardium for the induction of cardiomyocyte dedifferentiation and proliferation in adult zebrafish hearts,,,WT,,WT,,strain:EKW|breed:n1|cultivar:n1|ecotype:n1|dev stage:Adult|sex:pooled male and female|tissue:hearts|genotype:WT|sample type:tissue sample|treatment:untreated|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish cardiac tissue,WT1 RNASEQ,WT1 RNASEQ,Tissue was resuspended in 700ul Trizol and total RNA was extracted using miRNeasy kit following manufacturers description. Total RNA integrity was assessed and quantified on a RNA nano Agilent chip following manufacturers description. RNA libraries were prepared 500ng input using the Kapa stranded RNA Seq kit using the oligo dT module to enrich for mRNA transcripts. Libraries were pooled to equimolar concentrations and sequenced on an Illumina HiSeq2500 paired end reads using v4 high output chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP211964,,,CCB6CANXX_5_180204_CFL--008_Other_TAGCTT_R_180116_DAVHUM_LIB2500_M003_R1.fastq.gz CCB6CANXX_5_180204_CFL--008_Other_TAGCTT_R_180116_DAVHUM_LIB2500_M003_R2.fastq.gz,fastq fastq,7309496000.0,29237984.0,CCB6CANXX 5 180204 CFL 008 Other TAGCTT R 180116 DAVHUM LIB2500 M003 R1.fastq.gz,0:125 1:125,A:2038562638;C:1607745758;G:1627387822;T:2033916634;N:1883148,125,125,,,2038562638,1607745758,1627387822,2033916634,1883148,SRX6362165,SRS5024084,SRA913571,Victor Chang Cardiac Research Institute|Genome core,Victor Chang Cardiac Research Institute,2,0.94874,0.95324,0.08149,0.08128,0.79356,0.79575,0.58607,0.5765,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2019-06-26,Adult,Adult,Heart,Cardiovascular System 52921,SRR9596465,SRX6362164,SRS5024084,SRP211964,PRJNA551130,Induction of adult cardiomyocyte renewal by Klf1,PRJNA551130,Other,In highly regenerative animals cardiac regeneration occurs innately through cardiomyocyte dedifferentiation and proliferation although the regenerative mechanisms remain unclear. This project contains raw sequencing data sets that were used to identify that klf1 a Kruppel like transcription factor essential for red blood cell development is also necessary and sufficient in the myocardium for the induction of cardiomyocyte dedifferentiation and proliferation in adult zebrafish hearts,,,WT,,WT,,strain:EKW|breed:n1|cultivar:n1|ecotype:n1|dev stage:Adult|sex:pooled male and female|tissue:hearts|genotype:WT|sample type:tissue sample|treatment:untreated|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish cardiac tissue,WT2 RNASEQ,WT2 RNASEQ,Tissue was resuspended in 700ul Trizol and total RNA was extracted using miRNeasy kit following manufacturers description. Total RNA integrity was assessed and quantified on a RNA nano Agilent chip following manufacturers description. RNA libraries were prepared 500ng input using the Kapa stranded RNA Seq kit using the oligo dT module to enrich for mRNA transcripts. Libraries were pooled to equimolar concentrations and sequenced on an Illumina HiSeq2500 paired end reads using v4 high output chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP211964,,,CCB6CANXX_5_180204_CFL--009_Other_GGCTAC_R_180116_DAVHUM_LIB2500_M003_R1.fastq.gz CCB6CANXX_5_180204_CFL--009_Other_GGCTAC_R_180116_DAVHUM_LIB2500_M003_R2.fastq.gz,fastq fastq,6324176500.0,25296706.0,CCB6CANXX 5 180204 CFL 009 Other GGCTAC R 180116 DAVHUM LIB2500 M003 R1.fastq.gz,0:125 1:125,A:1766296515;C:1389598935;G:1403023173;T:1763639041;N:1618836,125,125,,,1766296515,1389598935,1403023173,1763639041,1618836,SRX6362164,SRS5024084,SRA913571,Victor Chang Cardiac Research Institute|Genome core,Victor Chang Cardiac Research Institute,2,0.94374,0.94892,0.09048,0.09084,0.78681,0.79066,0.57761,0.5755,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2019-06-26,Adult,Adult,Heart,Cardiovascular System 52922,SRR9596466,SRX6362163,SRS5024084,SRP211964,PRJNA551130,Induction of adult cardiomyocyte renewal by Klf1,PRJNA551130,Other,In highly regenerative animals cardiac regeneration occurs innately through cardiomyocyte dedifferentiation and proliferation although the regenerative mechanisms remain unclear. This project contains raw sequencing data sets that were used to identify that klf1 a Kruppel like transcription factor essential for red blood cell development is also necessary and sufficient in the myocardium for the induction of cardiomyocyte dedifferentiation and proliferation in adult zebrafish hearts,,,WT,,WT,,strain:EKW|breed:n1|cultivar:n1|ecotype:n1|dev stage:Adult|sex:pooled male and female|tissue:hearts|genotype:WT|sample type:tissue sample|treatment:untreated|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish cardiac tissue,WT3 RNASEQ,WT3 RNASEQ,Tissue was resuspended in 700ul Trizol and total RNA was extracted using miRNeasy kit following manufacturers description. Total RNA integrity was assessed and quantified on a RNA nano Agilent chip following manufacturers description. RNA libraries were prepared 500ng input using the Kapa stranded RNA Seq kit using the oligo dT module to enrich for mRNA transcripts. Libraries were pooled to equimolar concentrations and sequenced on an Illumina HiSeq2500 paired end reads using v4 high output chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP211964,,,CCB6CANXX_5_180204_CFL--010_Other_GTGGCC_R_180116_DAVHUM_LIB2500_M003_R1.fastq.gz CCB6CANXX_5_180204_CFL--010_Other_GTGGCC_R_180116_DAVHUM_LIB2500_M003_R2.fastq.gz,fastq fastq,7057191250.0,28228765.0,CCB6CANXX 5 180204 CFL 010 Other GTGGCC R 180116 DAVHUM LIB2500 M003 R1.fastq.gz,0:125 1:125,A:1983309478;C:1539045596;G:1559191474;T:1973857420;N:1787282,125,125,,,1983309478,1539045596,1559191474,1973857420,1787282,SRX6362163,SRS5024084,SRA913571,Victor Chang Cardiac Research Institute|Genome core,Victor Chang Cardiac Research Institute,2,0.94841,0.95328,0.08661,0.08555,0.78936,0.79243,0.58731,0.61025,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2019-06-26,Adult,Adult,Heart,Cardiovascular System 52923,SRR9596467,SRX6362162,SRS5024084,SRP211964,PRJNA551130,Induction of adult cardiomyocyte renewal by Klf1,PRJNA551130,Other,In highly regenerative animals cardiac regeneration occurs innately through cardiomyocyte dedifferentiation and proliferation although the regenerative mechanisms remain unclear. This project contains raw sequencing data sets that were used to identify that klf1 a Kruppel like transcription factor essential for red blood cell development is also necessary and sufficient in the myocardium for the induction of cardiomyocyte dedifferentiation and proliferation in adult zebrafish hearts,,,WT,,WT,,strain:EKW|breed:n1|cultivar:n1|ecotype:n1|dev stage:Adult|sex:pooled male and female|tissue:hearts|genotype:WT|sample type:tissue sample|treatment:untreated|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of zebrafish cardiac tissue,WT4 RNASEQ,WT4 RNASEQ,Tissue was resuspended in 700ul Trizol and total RNA was extracted using miRNeasy kit following manufacturers description. Total RNA integrity was assessed and quantified on a RNA nano Agilent chip following manufacturers description. RNA libraries were prepared 500ng input using the Kapa stranded RNA Seq kit using the oligo dT module to enrich for mRNA transcripts. Libraries were pooled to equimolar concentrations and sequenced on an Illumina HiSeq2500 paired end reads using v4 high output chemistry.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina HiSeq 2500,,SRP211964,,,CCB6CANXX_5_180204_CFL--011_Other_GTTTCG_R_180116_DAVHUM_LIB2500_M003_R1.fastq.gz CCB6CANXX_5_180204_CFL--011_Other_GTTTCG_R_180116_DAVHUM_LIB2500_M003_R2.fastq.gz,fastq fastq,6296219250.0,25184877.0,CCB6CANXX 5 180204 CFL 011 Other GTTTCG R 180116 DAVHUM LIB2500 M003 R1.fastq.gz,0:125 1:125,A:1758686297;C:1380462937;G:1398800047;T:1756652381;N:1617588,125,125,,,1758686297,1380462937,1398800047,1756652381,1617588,SRX6362162,SRS5024084,SRA913571,Victor Chang Cardiac Research Institute|Genome core,Victor Chang Cardiac Research Institute,2,0.94465,0.94985,0.09014,0.08958,0.78151,0.78472,0.58358,0.58306,125,125,B,B,biological fallback assumption,illumina,hiseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Australia,2019-06-26,Adult,Adult,Heart,Cardiovascular System 68887,SRR18218065,SRX14364509,SRS12177804,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,CG1 P2mut STABLE 5,,strain:CG1|age:133 days|sex:not collected|tissue:lymphoid|birth date:12 04 2017|death date:23 08 2017|genotype:rag2:hIL7R mut2 tdTomato|biological replicate:CG1 P2mut STABLE biologicalreplicate 5|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia stably expressing human mutant IL7R CG1,CG1 P2mut STABLE 5,CG1 P2mut STABLE 5,CG1 zebrafish stably expressing human mutant IL7R were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAURAAPEI-P51E3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAURAAPEI-P51E3_2.fq.gz,fastq fastq,18195264000.0,60650880.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAURAAPEI P51E3 1.fq.gz,0:150 1:150,A:4675448937;C:4456563746;G:4459950645;T:4603273696;N:26976,150,150,,,4675448937,4456563746,4459950645,4603273696,26976,SRX14364509,SRS12177804,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94521,0.94594,0.11243,0.11174,0.79551,0.79496,0.51393,0.51099,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Adult,Adult,Lymphatic System,Cardiovascular System 68888,SRR18218066,SRX14364508,SRS12177803,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,CG1 P2mut STABLE 4,,strain:CG1|age:133 days|sex:not collected|tissue:lymphoid|birth date:12 04 2017|death date:23 08 2017|genotype:rag2:hIL7R mut2 tdTomato|biological replicate:CG1 P2mut STABLE biologicalreplicate 4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia stably expressing human mutant IL7R CG1,CG1 P2mut STABLE 4,CG1 P2mut STABLE 4,CG1 zebrafish stably expressing human mutant IL7R were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAATRAAPEI-P39D3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAATRAAPEI-P39D3_2.fq.gz,fastq fastq,18145191600.0,60483972.0,FCHT5GHDSXX L1 HKRDZEBmfpEAATRAAPEI P39D3 1.fq.gz,0:150 1:150,A:4669829222;C:4433244502;G:4437119015;T:4604972909;N:25952,150,150,,,4669829222,4433244502,4437119015,4604972909,25952,SRX14364508,SRS12177803,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94405,0.94389,0.11135,0.11157,0.79401,0.79385,0.50436,0.50132,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Adult,Adult,Lymphatic System,Cardiovascular System 68893,SRR18218072,SRX14364503,SRS12177798,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc 7,,strain:Tu/AB|age:41 days|sex:not collected|tissue:lymphoid|birth date:04 11 2016|death date:15 12 2016|genotype:rag2:mCherry rag2:mMyc|biological replicate:Tu AB mMyc biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc Tu/AB,Tu AB mMyc 7,Tu AB mMyc 7,Tu/AB zebrafish overexpressing mouse Myc transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAXRAAPEI-P87H3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAXRAAPEI-P87H3_2.fq.gz,fastq fastq,18002105400.0,60007018.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAXRAAPEI P87H3 1.fq.gz,0:150 1:150,A:4483057959;C:4549819065;G:4562924506;T:4406277865;N:26005,150,150,,,4483057959,4549819065,4562924506,4406277865,26005,SRX14364503,SRS12177798,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.9259,0.92681,0.09642,0.09697,0.82479,0.82546,0.50634,0.5148,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Juvenile,Juvenile,Lymphatic System,Cardiovascular System 68894,SRR18218073,SRX14364502,SRS12177797,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc 6,,strain:Tu/AB|age:42 days|sex:not collected|tissue:lymphoid|birth date:03 11 2016|death date:15 12 2016|genotype:rag2:mCherry rag2:mMyc|biological replicate:Tu AB mMyc biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc Tu/AB,Tu AB mMyc 6,Tu AB mMyc 6,Tu/AB zebrafish overexpressing mouse Myc transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAWRABPEI-P75G3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAWRABPEI-P75G3_2.fq.gz,fastq fastq,18085463400.0,60284878.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAWRABPEI P75G3 1.fq.gz,0:150 1:150,A:4716166539;C:4371919988;G:4399782048;T:4597568953;N:25872,150,150,,,4716166539,4371919988,4399782048,4597568953,25872,SRX14364502,SRS12177797,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.90432,0.90596,0.06444,0.06367,0.80048,0.80095,0.51671,0.51624,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Juvenile,Juvenile,Lymphatic System,Cardiovascular System 68895,SRR18218074,SRX14364501,SRS12177796,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc 5,,strain:Tu/AB|age:42 days|sex:not collected|tissue:lymphoid|birth date:03 11 2016|death date:15 12 2016|genotype:rag2:mCherry rag2:mMyc|biological replicate:Tu AB mMyc biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc Tu/AB,Tu AB mMyc 5,Tu AB mMyc 5,Tu/AB zebrafish overexpressing mouse Myc transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAVRAAPEI-P63F3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAVRAAPEI-P63F3_2.fq.gz,fastq fastq,18063312600.0,60211042.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAVRAAPEI P63F3 1.fq.gz,0:150 1:150,A:4440821008;C:4618318980;G:4635597240;T:4368548938;N:26434,150,150,,,4440821008,4618318980,4635597240,4368548938,26434,SRX14364501,SRS12177796,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.91708,0.91735,0.0319,0.0316,0.80793,0.80744,0.50004,0.5071,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Juvenile,Juvenile,Lymphatic System,Cardiovascular System 68896,SRR18218075,SRX14364500,SRS12177795,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,CG1 P2mut STABLE 3,,strain:CG1|age:121 days|sex:not collected|tissue:lymphoid|birth date:12 04 2017|death date:11 08 2017|genotype:rag2:hIL7R mut2 tdTomato|biological replicate:CG1 P2mut STABLE biologicalreplicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia stably expressing human mutant IL7R CG1,CG1 P2mut STABLE 3,CG1 P2mut STABLE 3,CG1 zebrafish stably expressing human mutant IL7R were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAASRAAPEI-P27C3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAASRAAPEI-P27C3_2.fq.gz,fastq fastq,18163928100.0,60546427.0,FCHT5GHDSXX L1 HKRDZEBmfpEAASRAAPEI P27C3 1.fq.gz,0:150 1:150,A:4642188606;C:4470457895;G:4476885626;T:4574370149;N:25824,150,150,,,4642188606,4470457895,4476885626,4574370149,25824,SRX14364500,SRS12177795,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94449,0.94468,0.0858,0.0861,0.77114,0.7696,0.52498,0.52464,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Adult,Adult,Lymphatic System,Cardiovascular System 68897,SRR18218076,SRX14364499,SRS12177794,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc+P2mut 4,,strain:Tu/AB|age:28 days|sex:not collected|tissue:lymphoid|birth date:08 02 2017|death date:08 03 2017|genotype:rag2:mCherry rag2:mMyc rag2:hIL7R mut2|biological replicate:Tu AB mMyc+P1mut biological replicate 4|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc and human mutant IL7R Tu/AB,Tu AB mMyc+P2mut 4,Tu AB mMyc+P2mut 4,Tu/AB zebrafish overexpressing mouse Myc and human mutant IL7R transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEABBRAAPEI-P40D4_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEABBRAAPEI-P40D4_2.fq.gz,fastq fastq,18117791400.0,60392638.0,FCHT5GHDSXX L1 HKRDZEBmfpEABBRAAPEI P40D4 1.fq.gz,0:150 1:150,A:4565894721;C:4513701269;G:4551999162;T:4486169550;N:26698,150,150,,,4565894721,4513701269,4551999162,4486169550,26698,SRX14364499,SRS12177794,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94,0.93956,0.08699,0.08679,0.81941,0.81832,0.51722,0.51946,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Larval,Larval,Lymphatic System,Cardiovascular System 68898,SRR18218077,SRX14364498,SRS12177793,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc+P1mut 6,,strain:Tu/AB|age:35 days|sex:not collected|tissue:lymphoid|birth date:30 08 2016|death date:04 10 2016|genotype:rag2:mCherry rag2:mMyc rag2:hIL7R mut1|biological replicate:Tu AB mMyc+P1mut biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc and human mutant IL7R Tu/AB,Tu AB mMyc+P1mut 6,Tu AB mMyc+P1mut 6,Tu/AB zebrafish overexpressing mouse Myc and human mutant IL7R transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEABARAAPEI-P28C4_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEABARAAPEI-P28C4_2.fq.gz,fastq fastq,18034321800.0,60114406.0,FCHT5GHDSXX L1 HKRDZEBmfpEABARAAPEI P28C4 1.fq.gz,0:150 1:150,A:4518122158;C:4519676234;G:4543758117;T:4452738564;N:26727,150,150,,,4518122158,4519676234,4543758117,4452738564,26727,SRX14364498,SRS12177793,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94431,0.94437,0.10494,0.10462,0.83177,0.83037,0.51143,0.51642,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Juvenile,Juvenile,Lymphatic System,Cardiovascular System 68899,SRR18218078,SRX14364497,SRS12177792,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc+P1mut 5,,strain:Tu/AB|age:35 days|sex:not collected|tissue:lymphoid|birth date:30 08 2016|death date:04 10 2016|genotype:rag2:mCherry rag2:mMyc rag2:hIL7R mut1|biological replicate:Tu AB mMyc+P1mut biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc and human mutant IL7R Tu/AB,Tu AB mMyc+P1mut 5,Tu AB mMyc+P1mut 5,Tu/AB zebrafish overexpressing mouse Myc and human mutant IL7R transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAZRAAPEI-P16B4_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAZRAAPEI-P16B4_2.fq.gz,fastq fastq,17750634300.0,59168781.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAZRAAPEI P16B4 1.fq.gz,0:150 1:150,A:4503506819;C:4398697723;G:4432972998;T:4415430837;N:25923,150,150,,,4503506819,4398697723,4432972998,4415430837,25923,SRX14364497,SRS12177792,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94306,0.94321,0.07511,0.0748,0.79837,0.79819,0.51326,0.50902,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Juvenile,Juvenile,Lymphatic System,Cardiovascular System 68900,SRR18218079,SRX14364496,SRS12177791,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,Tu AB mMyc+P1mut 4,,strain:Tu/AB|age:35 days|sex:not collected|tissue:lymphoid|birth date:30 08 2016|death date:04 10 2016|genotype:rag2:mCherry rag2:mMyc rag2:hIL7R mut1|biological replicate:Tu AB mMyc+P1mut biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia overexpressing mouse Myc and human mutant IL7R Tu/AB,Tu AB mMyc+P1mut 4,Tu AB mMyc+P1mut 4,Tu/AB zebrafish overexpressing mouse Myc and human mutant IL7R transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAYRAAPEI-P4A4_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAYRAAPEI-P4A4_2.fq.gz,fastq fastq,18063110700.0,60210369.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAYRAAPEI P4A4 1.fq.gz,0:150 1:150,A:4583950532;C:4496933352;G:4489104841;T:4493095718;N:26257,150,150,,,4583950532,4496933352,4489104841,4493095718,26257,SRX14364496,SRS12177791,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.95231,0.9534,0.12525,0.12554,0.84404,0.84323,0.52132,0.53078,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Juvenile,Juvenile,Lymphatic System,Cardiovascular System 68911,SRR18218090,SRX14364485,SRS12177780,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,CG1 P2mut STABLE 2,,strain:CG1|age:121 days|sex:not collected|tissue:lymphoid|birth date:12 04 2017|death date:11 08 2017|genotype:rag2:hIL7R mut2 tdTomato|biological replicate:CG1 P2mut STABLE biologicalreplicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia stably expressing human mutant IL7R CG1,CG1 P2mut STABLE 2,CG1 P2mut STABLE 2,CG1 zebrafish stably expressing human mutant IL7R were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAARRAAPEI-P15B3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAARRAAPEI-P15B3_2.fq.gz,fastq fastq,18103313700.0,60344379.0,FCHT5GHDSXX L1 HKRDZEBmfpEAARRAAPEI P15B3 1.fq.gz,0:150 1:150,A:4586370941;C:4481640272;G:4519408464;T:4515867439;N:26584,150,150,,,4586370941,4481640272,4519408464,4515867439,26584,SRX14364485,SRS12177780,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94376,0.94365,0.11084,0.10978,0.79847,0.79788,0.52621,0.52367,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Adult,Adult,Lymphatic System,Cardiovascular System 68912,SRR18218091,SRX14364484,SRS12177779,SRP362416,PRJNA812715,Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia,PRJNA812715,Other,T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.,,,,,CG1 P2mut STABLE 1,,strain:CG1|age:121 days|sex:not collected|tissue:lymphoid|birth date:12 04 2017|death date:11 08 2017|genotype:rag2:hIL7R mut2 tdTomato|biological replicate:CG1 P2mut STABLE biologicalreplicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio leukemia stably expressing human mutant IL7R CG1,CG1 P2mut STABLE 1,CG1 P2mut STABLE 1,CG1 zebrafish stably expressing human mutant IL7R were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.,,,RNA-Seq,TRANSCRIPTOMIC,PolyA,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,SRP362416,,,FCHT5GHDSXX_L1_HKRDZEBmfpEAAQRAAPEI-P3A3_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAQRAAPEI-P3A3_2.fq.gz,fastq fastq,18068692800.0,60228976.0,FCHT5GHDSXX L1 HKRDZEBmfpEAAQRAAPEI P3A3 1.fq.gz,0:150 1:150,A:4592071905;C:4477973011;G:4471601663;T:4527019823;N:26398,150,150,,,4592071905,4477973011,4471601663,4527019823,26398,SRX14364484,SRS12177779,SRA1380603,Instituto de Medicina Molecular Joao Lobo Antunes|JBarata lab,Instituto de Medicina Molecular Joao Lobo Antunes,2,0.94814,0.94931,0.09511,0.09463,0.79756,0.79762,0.51602,0.51609,150,150,B,B,biological fallback assumption,illumina,novaseq_era,unknown,poly_a,unknown,bulk,unknown,unknown,,Portugal,2022-03-04,Adult,Adult,Lymphatic System,Cardiovascular System