metadata: run_metadata: 6 rows where experiment.platform = "DNBSEQ", technology = "bulk" and tissue

6 rows where experiment.platform = "DNBSEQ", technology = "bulk" 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.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.extractprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	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.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
33934	33934	SRR30947094	SRX26349630	SRS22874784	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…	whole heart tak1+/+ wild type replicate #3	GSM8565205	source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1+/+\|geo loc name:missing\|collection date:missing	whole heart tak1+/+ wild type replicate #3	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	tissue:Whole heart 3 dpf\|genotype:tak1+/+	GSM8565205	GSM8565205: whole heart tak1+/+ wild type replicate #3; Danio rerio; RNA Seq	GSM8565205 r1	GSM8565205	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826	WT_3_1.fq.gz WT_3_2.fq.gz	fastq fastq	4449566200.0	22247831.0	GSM8565205 r1	0:100 1:100	A:1179341017;C:1046638560;G:1046356098;T:1177230525;N:0	100	100	1179341017	1046638560	1046356098	1177230525	0	SRX26349630	SRS22874784	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33935	33935	SRR30947095	SRX26349629	SRS22874783	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…	whole heart tak1+/+ wild type replicate #2	GSM8565204	source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1+/+\|geo loc name:missing\|collection date:missing	whole heart tak1+/+ wild type replicate #2	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	tissue:Whole heart 3 dpf\|genotype:tak1+/+	GSM8565204	GSM8565204: whole heart tak1+/+ wild type replicate #2; Danio rerio; RNA Seq	GSM8565204 r1	GSM8565204	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826	WT_2_1.fq.gz WT_2_2.fq.gz	fastq fastq	4519627600.0	22598138.0	GSM8565204 r1	0:100 1:100	A:1207344552;C:1055139553;G:1056806709;T:1200336786;N:0	100	100	1207344552	1055139553	1056806709	1200336786	0	SRX26349629	SRS22874783	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33936	33936	SRR30947096	SRX26349628	SRS22874781	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…	whole heart tak1+/+ wild type replicate #1	GSM8565203	source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1+/+\|geo loc name:missing\|collection date:missing	whole heart tak1+/+ wild type replicate #1	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	tissue:Whole heart 3 dpf\|genotype:tak1+/+	GSM8565203	GSM8565203: whole heart tak1+/+ wild type replicate #1; Danio rerio; RNA Seq	GSM8565203 r1	GSM8565203	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826	WT_1_1.fq.gz WT_1_2.fq.gz	fastq fastq	4496601200.0	22483006.0	GSM8565203 r1	0:100 1:100	A:1201390946;C:1050348674;G:1051355386;T:1193506194;N:0	100	100	1201390946	1050348674	1051355386	1193506194	0	SRX26349628	SRS22874781	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33937	33937	SRR30947097	SRX26349627	SRS22874780	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…	whole heart tak1 / mutant replicate #3	GSM8565202	source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1 / \|geo loc name:missing\|collection date:missing	whole heart tak1 / mutant replicate #3	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	tissue:Whole heart 3 dpf\|genotype:tak1 /	GSM8565202	GSM8565202: whole heart tak1 / mutant replicate #3; Danio rerio; RNA Seq	GSM8565202 r1	GSM8565202	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826	mut_3_1.fq.gz mut_3_2.fq.gz	fastq fastq	4451759600.0	22258798.0	GSM8565202 r1	0:100 1:100	A:1167798041;C:1064608876;G:1066460994;T:1152891689;N:0	100	100	1167798041	1064608876	1066460994	1152891689	0	SRX26349627	SRS22874780	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33938	33938	SRR30947098	SRX26349626	SRS22874782	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…	whole heart tak1 / mutant replicate #2	GSM8565201	source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1 / \|geo loc name:missing\|collection date:missing	whole heart tak1 / mutant replicate #2	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	tissue:Whole heart 3 dpf\|genotype:tak1 /	GSM8565201	GSM8565201: whole heart tak1 / mutant replicate #2; Danio rerio; RNA Seq	GSM8565201 r1	GSM8565201	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826	mut_2_1.fq.gz mut_2_2.fq.gz	fastq fastq	4534495200.0	22672476.0	GSM8565201 r1										SRX26349626	SRS22874782	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	Heart	Cardiovascular System
33939	33939	SRR30947099	SRX26349625	SRS22874779	SRP537826	PRJNA1171482	TAK1 operates at the primary cilium in non canonical TGFB/BMP signaling to control heart development	GSE279246	Transcriptome Analysis	Transforming Growth Factor Beta Activated Kinase 1 TAK1/MAP3K7 along with its upstream regulators TAK1 Binding Protein 2 TAB2 and the catalytic alpha subunit of Protein Kinase A PKA Ca/PRKACA has been identified as a pivotal player in regulation of developmental processes. Haploinsufficiency of TAB2 causes Congenital Heart Disease CHD and rare variants in PKA Ca and TAK1 cause cardioacrofacial dysplasia CAFD and Frontometaphyseal Dysplasia FMD and cardiospondylocarpofacial syndrome CSCFS respectively rare multisystem syndromes where CHD may appear in the clinical spectrum. We hypothesized that TAK1 plays a significant role in heart development and CHD and addressed this by genetic analysis in CHD patient cohorts and experiments in cell and animal models. Exome sequencing data from 1 471 CHD patients with extracardiac anomalies syndromic CHD sCHD 2 405 patients with nonsyndromic CHD nsCHD and 45 082 controls showed increased burden of rare TAB2 and TAK1 variants in sCHD but not in nsCHD. Detailed characterization of tak1 / and tab2 / zebrafish mutants revealed cardiac defects dilated atrium trabeculation defects tachycardia and reduced contractility as well as extracardiac developmental anomalies. RNA sequencing of tak1 / mutant hearts showed downregulation of genes encoding core cardiac transcription factors sarcomeric proteins and extracellular matrix proteins. Experiments with cell cultures and analysis of zebrafish larvae and gastruloids indicated that TAK1 via TAB2 and PKA Ca is activated at the primary cilium during cardiomyogenesis and that TAK1 activation at this site is enhanced by cardiomyogenic signaling molecules including ligands of the TGFB/BMP superfamily. Consistent with these findings CRISPR/Cas9 mediated editing of TAK1 or administration of small molecule inhibitors targeting TAK1 inhibited ciliary signaling and cardiomyocyte differentiation in vitro while FMD causing mutations in TAK1 reduced its ciliary localization. In conclusion our data establishes a central role for TAK1…	whole heart tak1 / mutant replicate #1	GSM8565200	source name:Whole heart 3 dpf\|tissue:Whole heart 3 dpf\|genotype:tak1 / \|geo loc name:missing\|collection date:missing	whole heart tak1 / mutant replicate #1	post quality filtering reads were aligned to reference sequence GCF 000002035.6 GRCz11 using HISAT and Bowtie 2. Average mapping ratio with reference genome was 88.50% average mapping ratio with genes was 74.56%. In total 23966 genes were identified. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: Matrix txt file. Columns: gene id NCBI; gene symbol; tpm mut 1; tpm mut 2; tpm mut 3; tpm WT 1; tpm WT 2; tpm WT 3. Data is shown as transcripts per million TPM.	Whole heart 3 dpf	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	tissue:Whole heart 3 dpf\|genotype:tak1 /	GSM8565200	GSM8565200: whole heart tak1 / mutant replicate #1; Danio rerio; RNA Seq	GSM8565200 r1	GSM8565200	1	RNA isolation using Qiagen Rneasy micro kit Bulk RNAseq was performed as a service by BGI China. Samples were paired end sequenced using the DNBSEQ platform.	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	DNBSEQ	DNBSEQ-G400	SRP537826	mut_1_1.fq.gz mut_1_2.fq.gz	fastq fastq	4425052600.0	22125263.0	GSM8565200 r1	0:100 1:100	A:1161989932;C:1055452567;G:1055912540;T:1151697561;N:0	100	100	1161989932	1055452567	1055912540	1151697561	0	SRX26349625	SRS22874779	SRA1990217	Department of Cellular and Molecular Medicine, University of Copenhagen	Department of Cellular and Molecular Medicine, University of Copenhagen	B	B	biological fallback assumption	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	bulk	bulk	Denmark	2024-10-10	Larval	Larval	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");;