metadata: run_metadata: 14 rows where experiment.library_selection = "PolyA", technology = "unknown" and tissue

14 rows where experiment.library_selection = "PolyA", technology = "unknown" and tissue_curation = "Heart"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.description	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
31715	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	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	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	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	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	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	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	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	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	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	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	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	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	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

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;