metadata: run_metadata: 9 rows where devstage_curation = "Larval" and tissue

9 rows where devstage_curation = "Larval" and tissue_curation = "Lymphatic System"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	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.attributes	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
61414	61414	SRR12712225	SRX9191123	SRS7427095	SRP285378	PRJNA665656	The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]	GSE158566	Transcriptome Analysis	The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos	parent bioproject:PRJNA748172	ddx21 sibling 02	GSM4802983	tissue:ddx21 sibling\|genotype/variation:ddx21 sibling\|abbreviatedname:Sib 02\|cell type:venous and lymphatic ECs VECs LECs	ddx21 sibling 02	Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample	ddx21 sibling	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	genotype/variation:ddx21 sibling\|abbreviatedname:Sib 02\|cell type:venous and lymphatic ECs VECs LECs	GSM4802983	GSM4802983: ddx21 sibling 02; Danio rerio; RNA Seq	GSM4802983		1	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4802983	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP285378	4-DDX_sibling2_S5_R1_001.fastq	fastq	4132086148.0	54841271.0	GSM4802983 r1	0:75.35 1:0	A:1143149123;C:915565985;G:945819940;T:1127493713;N:57387	75	0	1143149123	915565985	945819940	1127493713	57387	SRX9191123	SRS7427095	SRA1131557	GEO	Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre	1	0.93153		0.15182		0.73127		0.47996		75		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2020-09-25	Larval	Larval	Lymphatic System	Cardiovascular System
61415	61415	SRR12712224	SRX9191122	SRS7427094	SRP285378	PRJNA665656	The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]	GSE158566	Transcriptome Analysis	The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos	parent bioproject:PRJNA748172	ddx21 mutant 02	GSM4802982	tissue:ddx21 mutant\|genotype/variation:ddx21 mutant\|abbreviatedname:Mut 02\|cell type:venous and lymphatic ECs VECs LECs	ddx21 mutant 02	Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample	ddx21 mutant	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	genotype/variation:ddx21 mutant\|abbreviatedname:Mut 02\|cell type:venous and lymphatic ECs VECs LECs	GSM4802982	GSM4802982: ddx21 mutant 02; Danio rerio; RNA Seq	GSM4802982		1	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4802982	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP285378	3-DDX1_mutant2_S6_R1_001.fastq	fastq	4489565415.0	59577710.0	GSM4802982 r1	0:75.36 1:0	A:1250571429;C:986785347;G:1019382421;T:1232761308;N:64910	75	0	1250571429	986785347	1019382421	1232761308	64910	SRX9191122	SRS7427094	SRA1131557	GEO	Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre	1	0.93491		0.11271		0.7399		0.48877		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2020-09-25	Larval	Larval	Lymphatic System	Cardiovascular System
61416	61416	SRR12712223	SRX9191121	SRS7427093	SRP285378	PRJNA665656	The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]	GSE158566	Transcriptome Analysis	The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos	parent bioproject:PRJNA748172	ddx21 sibling 01	GSM4802981	tissue:ddx21 sibling\|genotype/variation:ddx21 sibling\|abbreviatedname:Sib 01\|cell type:venous and lymphatic ECs VECs LECs	ddx21 sibling 01	Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample	ddx21 sibling	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	genotype/variation:ddx21 sibling\|abbreviatedname:Sib 01\|cell type:venous and lymphatic ECs VECs LECs	GSM4802981	GSM4802981: ddx21 sibling 01; Danio rerio; RNA Seq	GSM4802981		1	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4802981	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP285378	2-DDX_sibling1_S7_R1_001.fastq	fastq	3962887115.0	52588574.0	GSM4802981 r1	0:75.36 1:0	A:1113967875;C:858353708;G:888913973;T:1101593170;N:58389	75	0	1113967875	858353708	888913973	1101593170	58389	SRX9191121	SRS7427093	SRA1131557	GEO	Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre	1	0.92594		0.17769		0.72143		0.49105		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2020-09-25	Larval	Larval	Lymphatic System	Cardiovascular System
61417	61417	SRR12712222	SRX9191120	SRS7427092	SRP285378	PRJNA665656	The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]	GSE158566	Transcriptome Analysis	The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos	parent bioproject:PRJNA748172	ddx21 mutant 01	GSM4802980	tissue:ddx21 mutant\|genotype/variation:ddx21 mutant\|abbreviatedname:Mut 01\|cell type:venous and lymphatic ECs VECs LECs	ddx21 mutant 01	Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample	ddx21 mutant	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	genotype/variation:ddx21 mutant\|abbreviatedname:Mut 01\|cell type:venous and lymphatic ECs VECs LECs	GSM4802980	GSM4802980: ddx21 mutant 01; Danio rerio; RNA Seq	GSM4802980		1	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4802980	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP285378	1-DDX1_mutant1_S8_R1_001.fastq	fastq	4172788466.0	55358419.0	GSM4802980 r1	0:75.38 1:0	A:1157297483;C:922321451;G:952921150;T:1140193401;N:54981	75	0	1157297483	922321451	952921150	1140193401	54981	SRX9191120	SRS7427092	SRA1131557	GEO	Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre	1	0.93753		0.11708		0.75022		0.4679		74		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2020-09-25	Larval	Larval	Lymphatic System	Cardiovascular System
61418	61418	SRR12712229	SRX9191119	SRS7427091	SRP285378	PRJNA665656	The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]	GSE158566	Transcriptome Analysis	The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos	parent bioproject:PRJNA748172	ddx21 sibling 04	GSM4802987	tissue:ddx21 sibling\|genotype/variation:ddx21 sibling\|abbreviatedname:Sib 04\|cell type:venous and lymphatic ECs VECs LECs	ddx21 sibling 04	Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample	ddx21 sibling	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	genotype/variation:ddx21 sibling\|abbreviatedname:Sib 04\|cell type:venous and lymphatic ECs VECs LECs	GSM4802987	GSM4802987: ddx21 sibling 04; Danio rerio; RNA Seq	GSM4802987		1	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4802987	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP285378	8-DDX_sibling4_S1_R1_001.fastq	fastq	4915017825.0	65191268.0	GSM4802987 r1	0:75.39 1:0	A:1371356175;C:1074769694;G:1111138012;T:1357694052;N:59892	75	0	1371356175	1074769694	1111138012	1357694052	59892	SRX9191119	SRS7427091	SRA1131557	GEO	Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre	1	0.93029		0.13059		0.76288		0.49579		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2020-09-25	Larval	Larval	Lymphatic System	Cardiovascular System
61419	61419	SRR12712228	SRX9191118	SRS7427090	SRP285378	PRJNA665656	The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]	GSE158566	Transcriptome Analysis	The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos	parent bioproject:PRJNA748172	ddx21 mutant 04	GSM4802986	tissue:ddx21 mutant\|genotype/variation:ddx21 mutant\|abbreviatedname:Mut 04\|cell type:venous and lymphatic ECs VECs LECs	ddx21 mutant 04	Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample	ddx21 mutant	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	genotype/variation:ddx21 mutant\|abbreviatedname:Mut 04\|cell type:venous and lymphatic ECs VECs LECs	GSM4802986	GSM4802986: ddx21 mutant 04; Danio rerio; RNA Seq	GSM4802986		1	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4802986	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP285378	7-DDX1_mutant4_S2_R1_001.fastq	fastq	4934798895.0	65454382.0	GSM4802986 r1	0:75.39 1:0	A:1386796418;C:1074595432;G:1108772428;T:1364575960;N:58657	75	0	1386796418	1074595432	1108772428	1364575960	58657	SRX9191118	SRS7427090	SRA1131557	GEO	Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre	1	0.93352		0.1274		0.75276		0.49744		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2020-09-25	Larval	Larval	Lymphatic System	Cardiovascular System
61420	61420	SRR12712227	SRX9191117	SRS7427089	SRP285378	PRJNA665656	The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]	GSE158566	Transcriptome Analysis	The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos	parent bioproject:PRJNA748172	ddx21 sibling 03	GSM4802985	tissue:ddx21 sibling\|genotype/variation:ddx21 sibling\|abbreviatedname:Sib 03\|cell type:venous and lymphatic ECs VECs LECs	ddx21 sibling 03	Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample	ddx21 sibling	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	genotype/variation:ddx21 sibling\|abbreviatedname:Sib 03\|cell type:venous and lymphatic ECs VECs LECs	GSM4802985	GSM4802985: ddx21 sibling 03; Danio rerio; RNA Seq	GSM4802985		1	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4802985	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP285378	6-DDX_sibling3_S3_R1_001.fastq	fastq	4686029757.0	62155887.0	GSM4802985 r1	0:75.39 1:0	A:1310041056;C:1025050637;G:1061770975;T:1289110659;N:56430	75	0	1310041056	1025050637	1061770975	1289110659	56430	SRX9191117	SRS7427089	SRA1131557	GEO	Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre	1	0.93421		0.13013		0.74468		0.50075		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2020-09-25	Larval	Larval	Lymphatic System	Cardiovascular System
61421	61421	SRR12712226	SRX9191116	SRS7427088	SRP285378	PRJNA665656	The RNA helicase Ddx21 controls Vegfc driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53 p21 signalling [zebrafish]	GSE158566	Transcriptome Analysis	The development of a differentiated and functional vasculature requires coordinated control of cell fate specification lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels we uncovered a mutant for the RNA helicase Ddx21. Ddx21 cell autonomously regulates the early development of lymphatic endothelial cells. Ddx21 is essential for Vegfc Vegfr3 driven endothelial cell proliferation. Ddx21 is an established regulator of ribosomal RNA transcription and in the absence of Ddx21 mutant lymphatic endothelial cells show reduced ribosome biogenesis. Ultimately loss of Ddx21 leads to a p53 p21 dependent cell cycle arrest that blocks embryonic lymphangiogenesis. Thus the RNA helicase Ddx21 coordinates the endothelial cell proliferative response to Vegfc Vegfr3 signalling by balancing ribosome biogenesis and p53 p21 signalling. This mechanism may have therapeutic potential in diseases of excessive lymphangiogenesis such as in cancer metastasis or lymphatic malformation. Overall design: LEC and VEC RNA profiles on sibling and ddx21 mutant cells obtained from zebrafish embryos	parent bioproject:PRJNA748172	ddx21 mutant 03	GSM4802984	tissue:ddx21 mutant\|genotype/variation:ddx21 mutant\|abbreviatedname:Mut 03\|cell type:venous and lymphatic ECs VECs LECs	ddx21 mutant 03	Sequenced reads were assessed for quality using fastqc and aligned and summarized using Subread V2.0.0 functions align and featureCount with default settings Filtering and normalisation of tag counts performed in edgeR using sequential functions filterByExpr calcNormFactors and cpm A batch effect was removed in edgeR using removeBatchEffect function For plotting and differential expression analysis an offset of +1.0 and log2 transformation was applied Genome build: GRCz11 GCA 000002035.4 Supplementary files format and content: Matrix table with normalised batch corredted and log2 transformed CPM for every gene and every sample	ddx21 mutant	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	genotype/variation:ddx21 mutant\|abbreviatedname:Mut 03\|cell type:venous and lymphatic ECs VECs LECs	GSM4802984	GSM4802984: ddx21 mutant 03; Danio rerio; RNA Seq	GSM4802984		1	At 3 dpf double positve cells were sorted from Tgfli1a:nEGFP;Tg5.2lyve1b:DsRed to isolate LECs and VECs RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM4802984	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina HiSeq 2000	SRP285378	5-DDX1_mutant3_S4_R1_001.fastq	fastq	4774244717.0	63335788.0	GSM4802984 r1	0:75.38 1:0	A:1333800977;C:1045188899;G:1081436862;T:1313758360;N:59619	75	0	1333800977	1045188899	1081436862	1313758360	59619	SRX9191116	SRS7427088	SRA1131557	GEO	Hogan Laboratory, Program in Organogenesis and Cancer, Peter MacCallum Cancer Centre	1	0.93177		0.13392		0.73864		0.49841		76		B		usable mapping rate	illumina	hiseq_era	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	Australia	2020-09-25	Larval	Larval	Lymphatic System	Cardiovascular System
68897	68897	SRR18218076	SRX14364499	SRS12177794	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.			Tu AB mMyc+P2mut 4	strain:Tu/AB\|age:28 days\|sex:not collected\|tissue:lymphoid\|birth date:08 02 2017\|death date:08 03 2017\|genotype:rag2:mCherry rag2:mMyc rag2:hIL7R mut2\|biological replicate:Tu AB mMyc+P1mut biological replicate 4\|BioSampleModel:Model organism or animal							RNA seq of Danio rerio leukemia overexpressing mouse Myc and human mutant IL7R Tu/AB	Tu AB mMyc+P2mut 4	Tu AB mMyc+P2mut 4	Tu/AB zebrafish overexpressing mouse Myc and human mutant IL7R transiently were sacrificed when moribund and sorted leukemias were harvested for further analysis. The RNA was extracted from sorted cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416	FCHT5GHDSXX_L1_HKRDZEBmfpEABBRAAPEI-P40D4_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEABBRAAPEI-P40D4_2.fq.gz	fastq fastq	18117791400.0	60392638.0	FCHT5GHDSXX L1 HKRDZEBmfpEABBRAAPEI P40D4 1.fq.gz	0:150 1:150	A:4565894721;C:4513701269;G:4551999162;T:4486169550;N:26698	150	150	4565894721	4513701269	4551999162	4486169550	26698	SRX14364499	SRS12177794	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.94	0.93956	0.08699	0.08679	0.81941	0.81832	0.51722	0.51946	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Larval	Larval	Lymphatic System	Cardiovascular System

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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");;