{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"PolyA\", experiment.library_source = \"TRANSCRIPTOMIC\" and tissue_curation = \"Heart\"", "rows": [[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", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C 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 \u03bcg/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\u00b0C 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\u00b0C 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 \u03bcg/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", null, null, null, null, null, null, null, null, "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\u00b0C 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 \u03bcg/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\u00b0C 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\u00b0C 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 \u03bcg/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", null, "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, null, null, 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", null, "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", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C 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 \u03bcg/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\u00b0C 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\u00b0C 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 \u03bcg/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", null, null, null, null, null, null, null, null, "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\u00b0C 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 \u03bcg/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\u00b0C 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\u00b0C 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 \u03bcg/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", null, "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, null, null, 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", null, "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", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C 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 \u03bcg/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\u00b0C 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\u00b0C 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 \u03bcg/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", null, null, null, null, null, null, null, null, "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\u00b0C 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 \u03bcg/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\u00b0C 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\u00b0C 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 \u03bcg/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", null, "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, null, null, 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", null, "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", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C 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 \u03bcg/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\u00b0C 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\u00b0C 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 \u03bcg/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", null, null, null, null, null, null, null, null, "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\u00b0C 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 \u03bcg/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\u00b0C 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\u00b0C 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 \u03bcg/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", null, "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, null, null, 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", null, "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", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C 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 \u03bcg/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\u00b0C 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\u00b0C 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 \u03bcg/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", null, null, null, null, null, null, null, null, "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\u00b0C 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 \u03bcg/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\u00b0C 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\u00b0C 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 \u03bcg/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", null, "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, null, null, 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", null, "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", null, "Protocols: Following laser injury at 72 hpf Tgmyl7:gal4::GFP;UAS:mRFP larvae were incubated at 28.5\u00b0C 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 \u03bcg/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\u00b0C 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\u00b0C 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 \u03bcg/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", null, null, null, null, null, null, null, null, "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\u00b0C 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 \u03bcg/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\u00b0C 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\u00b0C 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 \u03bcg/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", null, "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, null, null, 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", null, "United Kingdom", "2021-10-01", "Larval", "Larval", "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.", null, null, null, "myh6+/  3", "Sample 6", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498846", null, null, "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, null, null, 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", null, "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.", null, null, null, "myh6+/  2", "Sample 5", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498846", null, null, "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, null, null, 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", null, "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.", null, null, null, "myh6+/  1", "Sample 4", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498846", null, null, "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, null, null, 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", null, "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.", null, null, null, "WT 3", "Sample 3", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498846", null, null, "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, null, null, 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", null, "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.", null, null, null, "WT 2", "Sample 2", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498846", null, null, "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, null, null, 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", null, "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.", null, null, null, "WT 1", "Sample 1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP498846", null, null, "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, null, null, 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", null, "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", null, null, "klf1 over expressing", null, "klf1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP211964", null, null, "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, null, null, 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", null, "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", null, null, "klf1 over expressing", null, "klf1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP211964", null, null, "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, null, null, 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", null, "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", null, null, "klf1 over expressing", null, "klf1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP211964", null, null, "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, null, null, 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", null, "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", null, null, "klf1 over expressing", null, "klf1", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP211964", null, null, "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, null, null, 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", null, "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", null, null, "WT", null, "WT", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP211964", null, null, "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, null, null, 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", null, "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", null, null, "WT", null, "WT", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP211964", null, null, "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, null, null, 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", null, "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", null, null, "WT", null, "WT", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP211964", null, null, "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, null, null, 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", null, "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", null, null, "WT", null, "WT", null, "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", null, null, null, null, null, null, null, null, "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.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP211964", null, null, "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, null, null, 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", 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