metadata: run_metadata: 74 rows where experiment.library_selection = "cDNA", technology = "unknown" and tissue_curation

74 rows where experiment.library_selection = "cDNA", technology = "unknown" and tissue_curation_coarse = "Skeletal Element"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.attributes	study.PMIDs	sample.description	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	GEOsample.treatmentprotocol	GEOsample.extractprotocol	GEOsample.growthprotocol	GEOsample.characteristics	GEOsample.accession	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_construction_protocol	experiment.attributes	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.spot_descriptor	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.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
29165	29165	SRR27180613	SRX22861017	SRS19836056	SRP477408	PRJNA1051145	laser captured chondrocyte transcriptomes from cranial base	GSE249932	Transcriptome Analysis	similar methods as in Gomez Picos et al. 2022 and Nguyen et al. 2023 Overall design: mRNA profiles of wild type Danio rerio chondrocytes		pubmed:38117077		Z6 WT	GSM7967333	source name:laser captured cartilage without xxx from cranial base in occipital region\|tissue:cartilage\|age:6dpf\|genotype:wild type\|geo loc name:missing\|collection date:missing	Z6 WT	The paired end Illumina reads were trimmed using Trimmomatic v0.36 Bolger et al. 2014. Mapped to the Danio rerio Zv9 fom Ensembl. TMM normalization Robinson and Oshlack 2010 was performed using edgeR. Cutoff of genes considered expressed was determined by calculationg the minimum value of the bimodal distribution of counts. Assembly: Danio rerio Ensembl Zv9 Supplementary files format and content: Comma delimited text file includes counts for wildtype samples	laser captured cartilage without xxx from cranial base in occipital region	N/A	RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer’s instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute Prime Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc..	standard conditions EM filled dishes at 28.5C	tissue:cartilage\|age:6dpf\|genotype:wild type	GSM7967333	GSM7967333: Z6 WT; Danio rerio; RNA Seq	GSM7967333 r1	GSM7967333	1	RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer's instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute Prime Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc..		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP477408		Z6_R1.fastq.gz Z6_R2.fastq.gz	fastq fastq	7236720902.0	35825351.0	GSM7967333 r1	0:101 1:101	A:2065141509;C:1515489646;G:1508477450;T:2145425270;N:2187027	101	101	2065141509	1515489646	1508477450	2145425270	2187027	SRX22861017	SRS19836056	SRA1767043	3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan	3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan	2	0.92486	0.92406	0.2589	0.2586	0.81836	0.81937	0.64846	0.64959	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Canada	2023-12-11	Larval	Larval	Bone or Cartilage	Skeletal Element
29166	29166	SRR27180614	SRX22861016	SRS19836057	SRP477408	PRJNA1051145	laser captured chondrocyte transcriptomes from cranial base	GSE249932	Transcriptome Analysis	similar methods as in Gomez Picos et al. 2022 and Nguyen et al. 2023 Overall design: mRNA profiles of wild type Danio rerio chondrocytes		pubmed:38117077		Z3 WT	GSM7967332	source name:laser captured cartilage without xxx from cranial base in occipital region\|tissue:cartilage\|age:6dpf\|genotype:wild type\|geo loc name:missing\|collection date:missing	Z3 WT	The paired end Illumina reads were trimmed using Trimmomatic v0.36 Bolger et al. 2014. Mapped to the Danio rerio Zv9 fom Ensembl. TMM normalization Robinson and Oshlack 2010 was performed using edgeR. Cutoff of genes considered expressed was determined by calculationg the minimum value of the bimodal distribution of counts. Assembly: Danio rerio Ensembl Zv9 Supplementary files format and content: Comma delimited text file includes counts for wildtype samples	laser captured cartilage without xxx from cranial base in occipital region	N/A	RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer’s instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute Prime Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc..	standard conditions EM filled dishes at 28.5C	tissue:cartilage\|age:6dpf\|genotype:wild type	GSM7967332	GSM7967332: Z3 WT; Danio rerio; RNA Seq	GSM7967332 r1	GSM7967332	1	RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer's instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute Prime Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc..		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP477408		Z3_R1.fastq.gz Z3_R2.fastq.gz	fastq fastq	8154876754.0	40370677.0	GSM7967332 r1	0:101 1:101	A:2326535807;C:1739502467;G:1727655779;T:2358724699;N:2458002	101	101	2326535807	1739502467	1727655779	2358724699	2458002	SRX22861016	SRS19836057	SRA1767043	3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan	3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan	2	0.91893	0.92052	0.27086	0.27178	0.83489	0.83615	0.7337	0.73303	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Canada	2023-12-11	Larval	Larval	Bone or Cartilage	Skeletal Element
29167	29167	SRR27180615	SRX22861015	SRS19836055	SRP477408	PRJNA1051145	laser captured chondrocyte transcriptomes from cranial base	GSE249932	Transcriptome Analysis	similar methods as in Gomez Picos et al. 2022 and Nguyen et al. 2023 Overall design: mRNA profiles of wild type Danio rerio chondrocytes		pubmed:38117077		Z1 WT	GSM7967331	source name:laser captured cartilage without xxx from cranial base in occipital region\|tissue:cartilage\|age:6dpf\|genotype:wild type\|geo loc name:missing\|collection date:missing	Z1 WT	The paired end Illumina reads were trimmed using Trimmomatic v0.36 Bolger et al. 2014. Mapped to the Danio rerio Zv9 fom Ensembl. TMM normalization Robinson and Oshlack 2010 was performed using edgeR. Cutoff of genes considered expressed was determined by calculationg the minimum value of the bimodal distribution of counts. Assembly: Danio rerio Ensembl Zv9 Supplementary files format and content: Comma delimited text file includes counts for wildtype samples	laser captured cartilage without xxx from cranial base in occipital region	N/A	RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer’s instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute Prime Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc..	standard conditions EM filled dishes at 28.5C	tissue:cartilage\|age:6dpf\|genotype:wild type	GSM7967331	GSM7967331: Z1 WT; Danio rerio; RNA Seq	GSM7967331 r1	GSM7967331	1	RNA was isolated using the ARCTURUS PicoPure RNA Isolation Kit ThermoFisher Scientific; Cat# KIT0204 according to the manufacturer's instructions and DNase treatment was done using RNase Free DNase Qiagen; Cat#79254. RNA was amplified one round using MessageAmp II aRNA Kit ThermoFisher Scientific; Cat# AM1751. The RNA integrity was evaluated on the observation of a signature electropherogram pattern Bioanalyzer. A minimum of 5 10 ng of amplified RNA was used per sample for the construction of each library. RNA seq libraries were prepared by the National Research Council NRC Saskatoon using the Illumina TruSeq RNA Sample Prep Kit v2 with the following modification: the protocol was started at the Elute Prime Fragment step using5 µl amplified mRNA the minimum amount was 5 10 ng mRNA as determined using Quant iT RiboGreen RNA Assay Kit Invitrogen. The quality of each cDNA library was checked on a DNA 1000 chip using the 2100 Bioanalyzer Agilent Technologies Inc..		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP477408		Z1_R1.fastq.gz Z1_R2.fastq.gz	fastq fastq	9727948522.0	48158161.0	GSM7967331 r1	0:101 1:101	A:2710612972;C:2124743635;G:2101950141;T:2787702029;N:2939745	101	101	2710612972	2124743635	2101950141	2787702029	2939745	SRX22861015	SRS19836055	SRA1767043	3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan	3B14 HSC, Anatomy and Cell Biology, University of Saskatchewan	2	0.92553	0.92633	0.25474	0.25434	0.83362	0.83615	0.76464	0.75351	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Canada	2023-12-11	Larval	Larval	Bone or Cartilage	Skeletal Element
34618	34618	SRR32145149	SRX27491071	SRS23912869	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 4	GSM8760186	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760186	GSM8760186: kat6a Replicate 4; Danio rerio; RNA Seq	GSM8760186 r1	GSM8760186	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a4_S4_L001_R1_001.fastq.gz	fastq	1185101288.0	15593438.0	GSM8760186 r1	0:76	A:300559300;C:260467735;G:266433586;T:357432372;N:208295	76		300559300	260467735	266433586	357432372	208295	SRX27491071	SRS23912869	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34619	34619	SRR32145150	SRX27491071	SRS23912869	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 4	GSM8760186	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760186	GSM8760186: kat6a Replicate 4; Danio rerio; RNA Seq	GSM8760186 r1	GSM8760186	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a4_S4_L002_R1_001.fastq.gz	fastq	1131352948.0	14886223.0	GSM8760186 r2	0:76	A:286383575;C:248947288;G:254084926;T:341733278;N:203881	76		286383575	248947288	254084926	341733278	203881	SRX27491071	SRS23912869	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34620	34620	SRR32145151	SRX27491071	SRS23912869	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 4	GSM8760186	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760186	GSM8760186: kat6a Replicate 4; Danio rerio; RNA Seq	GSM8760186 r1	GSM8760186	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a4_S4_L003_R1_001.fastq.gz	fastq	1166160188.0	15344213.0	GSM8760186 r3	0:76	A:296592701;C:256034122;G:261605331;T:351825369;N:102665	76		296592701	256034122	261605331	351825369	102665	SRX27491071	SRS23912869	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34621	34621	SRR32145152	SRX27491071	SRS23912869	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 4	GSM8760186	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760186	GSM8760186: kat6a Replicate 4; Danio rerio; RNA Seq	GSM8760186 r1	GSM8760186	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a4_S4_L004_R1_001.fastq.gz	fastq	1123430480.0	14781980.0	GSM8760186 r4	0:76	A:285427665;C:246734929;G:251428534;T:339753027;N:86325	76		285427665	246734929	251428534	339753027	86325	SRX27491071	SRS23912869	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34622	34622	SRR32145153	SRX27491070	SRS23912868	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 3	GSM8760185	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760185	GSM8760185: kat6a Replicate 3; Danio rerio; RNA Seq	GSM8760185 r1	GSM8760185	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a3_S3_L001_R1_001.fastq.gz	fastq	1130086940.0	14869565.0	GSM8760185 r1	0:76	A:271600754;C:270119369;G:267701531;T:320468732;N:196554	76		271600754	270119369	267701531	320468732	196554	SRX27491070	SRS23912868	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34623	34623	SRR32145154	SRX27491070	SRS23912868	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 3	GSM8760185	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760185	GSM8760185: kat6a Replicate 3; Danio rerio; RNA Seq	GSM8760185 r1	GSM8760185	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a3_S3_L002_R1_001.fastq.gz	fastq	1084172604.0	14265429.0	GSM8760185 r2	0:76	A:260060383;C:259442661;G:256603224;T:307867713;N:198623	76		260060383	259442661	256603224	307867713	198623	SRX27491070	SRS23912868	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34624	34624	SRR32145155	SRX27491070	SRS23912868	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 3	GSM8760185	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760185	GSM8760185: kat6a Replicate 3; Danio rerio; RNA Seq	GSM8760185 r1	GSM8760185	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a3_S3_L003_R1_001.fastq.gz	fastq	1110196904.0	14607854.0	GSM8760185 r3	0:76	A:267507867;C:265237928;G:262455688;T:314899764;N:95657	76		267507867	265237928	262455688	314899764	95657	SRX27491070	SRS23912868	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34625	34625	SRR32145156	SRX27491070	SRS23912868	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 3	GSM8760185	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760185	GSM8760185: kat6a Replicate 3; Danio rerio; RNA Seq	GSM8760185 r1	GSM8760185	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a3_S3_L004_R1_001.fastq.gz	fastq	1075741468.0	14154493.0	GSM8760185 r4	0:76	A:259028301;C:257097498;G:253796080;T:305738292;N:81297	76		259028301	257097498	253796080	305738292	81297	SRX27491070	SRS23912868	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34626	34626	SRR32145157	SRX27491069	SRS23912867	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 2	GSM8760184	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760184	GSM8760184: kat6a Replicate 2; Danio rerio; RNA Seq	GSM8760184 r1	GSM8760184	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a2_S2_L001_R1_001.fastq.gz	fastq	1020140400.0	13422900.0	GSM8760184 r1	0:76	A:246705959;C:238000533;G:239066122;T:296188699;N:179087	76		246705959	238000533	239066122	296188699	179087	SRX27491069	SRS23912867	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34627	34627	SRR32145158	SRX27491069	SRS23912867	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 2	GSM8760184	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760184	GSM8760184: kat6a Replicate 2; Danio rerio; RNA Seq	GSM8760184 r1	GSM8760184	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a2_S2_L002_R1_001.fastq.gz	fastq	977643632.0	12863732.0	GSM8760184 r2	0:76	A:235933957;C:228339408;G:228898216;T:284296721;N:175330	76		235933957	228339408	228898216	284296721	175330	SRX27491069	SRS23912867	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34628	34628	SRR32145159	SRX27491069	SRS23912867	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 2	GSM8760184	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760184	GSM8760184: kat6a Replicate 2; Danio rerio; RNA Seq	GSM8760184 r1	GSM8760184	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a2_S2_L003_R1_001.fastq.gz	fastq	1003014712.0	13197562.0	GSM8760184 r3	0:76	A:243233308;C:233802542;G:234581740;T:291313383;N:83739	76		243233308	233802542	234581740	291313383	83739	SRX27491069	SRS23912867	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34629	34629	SRR32145160	SRX27491069	SRS23912867	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 2	GSM8760184	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760184	GSM8760184: kat6a Replicate 2; Danio rerio; RNA Seq	GSM8760184 r1	GSM8760184	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a2_S2_L004_R1_001.fastq.gz	fastq	971822564.0	12787139.0	GSM8760184 r4	0:76	A:235490570;C:226606386;G:226825751;T:282823868;N:75989	76		235490570	226606386	226825751	282823868	75989	SRX27491069	SRS23912867	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34630	34630	SRR32145161	SRX27491068	SRS23912866	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 1	GSM8760183	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760183	GSM8760183: kat6a Replicate 1; Danio rerio; RNA Seq	GSM8760183 r1	GSM8760183	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a1_S1_L001_R1_001.fastq.gz	fastq	1199414140.0	15781765.0	GSM8760183 r1	0:76	A:302128648;C:264050936;G:275501956;T:357525321;N:207279	76		302128648	264050936	275501956	357525321	207279	SRX27491068	SRS23912866	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34631	34631	SRR32145162	SRX27491068	SRS23912866	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 1	GSM8760183	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760183	GSM8760183: kat6a Replicate 1; Danio rerio; RNA Seq	GSM8760183 r1	GSM8760183	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a1_S1_L002_R1_001.fastq.gz	fastq	1146031360.0	15079360.0	GSM8760183 r2	0:76	A:288111631;C:252600982;G:262972849;T:342138841;N:207057	76		288111631	252600982	262972849	342138841	207057	SRX27491068	SRS23912866	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34632	34632	SRR32145163	SRX27491068	SRS23912866	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 1	GSM8760183	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760183	GSM8760183: kat6a Replicate 1; Danio rerio; RNA Seq	GSM8760183 r1	GSM8760183	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a1_S1_L003_R1_001.fastq.gz	fastq	1179501760.0	15519760.0	GSM8760183 r3	0:76	A:297785533;C:259437124;G:270403974;T:351772505;N:102624	76		297785533	259437124	270403974	351772505	102624	SRX27491068	SRS23912866	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34633	34633	SRR32145164	SRX27491068	SRS23912866	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				kat6a Replicate 1	GSM8760183	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	kat6a Replicate 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:kat6a; Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760183	GSM8760183: kat6a Replicate 1; Danio rerio; RNA Seq	GSM8760183 r1	GSM8760183	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		kat6a1_S1_L004_R1_001.fastq.gz	fastq	1138207844.0	14976419.0	GSM8760183 r4	0:76	A:287208643;C:250440049;G:260378372;T:340095505;N:85275	76		287208643	250440049	260378372	340095505	85275	SRX27491068	SRS23912866	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34634	34634	SRR32145165	SRX27491067	SRS23912865	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 4	GSM8760182	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760182	GSM8760182: WT Replicate 4; Danio rerio; RNA Seq	GSM8760182 r1	GSM8760182	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT3_S8_L001_R1_001.fastq.gz	fastq	1105608708.0	14547483.0	GSM8760182 r1	0:76	A:275003530;C:255171379;G:257731739;T:317503855;N:198205	76		275003530	255171379	257731739	317503855	198205	SRX27491067	SRS23912865	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34635	34635	SRR32145166	SRX27491067	SRS23912865	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 4	GSM8760182	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760182	GSM8760182: WT Replicate 4; Danio rerio; RNA Seq	GSM8760182 r1	GSM8760182	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT3_S8_L002_R1_001.fastq.gz	fastq	1057949108.0	13920383.0	GSM8760182 r2	0:76	A:262643868;C:244445110;G:246372974;T:304292800;N:194356	76		262643868	244445110	246372974	304292800	194356	SRX27491067	SRS23912865	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34636	34636	SRR32145167	SRX27491067	SRS23912865	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 4	GSM8760182	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760182	GSM8760182: WT Replicate 4; Danio rerio; RNA Seq	GSM8760182 r1	GSM8760182	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT3_S8_L003_R1_001.fastq.gz	fastq	1087749848.0	14312498.0	GSM8760182 r3	0:76	A:271320835;C:250818322;G:253044246;T:312473326;N:93119	76		271320835	250818322	253044246	312473326	93119	SRX27491067	SRS23912865	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34637	34637	SRR32145168	SRX27491067	SRS23912865	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 4	GSM8760182	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 4	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760182	GSM8760182: WT Replicate 4; Danio rerio; RNA Seq	GSM8760182 r1	GSM8760182	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT3_S8_L004_R1_001.fastq.gz	fastq	1051964032.0	13841632.0	GSM8760182 r4	0:76	A:262165724;C:242738788;G:244236708;T:302743784;N:79028	76		262165724	242738788	244236708	302743784	79028	SRX27491067	SRS23912865	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34638	34638	SRR32145169	SRX27491066	SRS23912864	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 3	GSM8760181	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760181	GSM8760181: WT Replicate 3; Danio rerio; RNA Seq	GSM8760181 r1	GSM8760181	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT3_S7_L001_R1_001.fastq.gz	fastq	1039833292.0	13682017.0	GSM8760181 r1	0:76	A:250507910;C:247806634;G:245922610;T:295415371;N:180767	76		250507910	247806634	245922610	295415371	180767	SRX27491066	SRS23912864	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34639	34639	SRR32145170	SRX27491066	SRS23912864	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 3	GSM8760181	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760181	GSM8760181: WT Replicate 3; Danio rerio; RNA Seq	GSM8760181 r1	GSM8760181	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT3_S7_L002_R1_001.fastq.gz	fastq	997262196.0	13121871.0	GSM8760181 r2	0:76	A:239743869;C:237950132;G:235660496;T:283726570;N:181129	76		239743869	237950132	235660496	283726570	181129	SRX27491066	SRS23912864	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34640	34640	SRR32145171	SRX27491066	SRS23912864	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 3	GSM8760181	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760181	GSM8760181: WT Replicate 3; Danio rerio; RNA Seq	GSM8760181 r1	GSM8760181	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT3_S7_L003_R1_001.fastq.gz	fastq	1021625592.0	13442442.0	GSM8760181 r3	0:76	A:246769441;C:243242872;G:241137871;T:290388153;N:87255	76		246769441	243242872	241137871	290388153	87255	SRX27491066	SRS23912864	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34641	34641	SRR32145172	SRX27491066	SRS23912864	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 3	GSM8760181	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 3	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760181	GSM8760181: WT Replicate 3; Danio rerio; RNA Seq	GSM8760181 r1	GSM8760181	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT3_S7_L004_R1_001.fastq.gz	fastq	988410400.0	13005400.0	GSM8760181 r4	0:76	A:238549859;C:235494730;G:232864346;T:281426699;N:74766	76		238549859	235494730	232864346	281426699	74766	SRX27491066	SRS23912864	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34642	34642	SRR32145173	SRX27491065	SRS23912863	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 2	GSM8760180	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760180	GSM8760180: WT Replicate 2; Danio rerio; RNA Seq	GSM8760180 r1	GSM8760180	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT2_S6_L001_R1_001.fastq.gz	fastq	1197864500.0	15761375.0	GSM8760180 r1	0:76	A:284440503;C:291285146;G:286388620;T:335544162;N:206069	76		284440503	291285146	286388620	335544162	206069	SRX27491065	SRS23912863	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34643	34643	SRR32145174	SRX27491065	SRS23912863	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 2	GSM8760180	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760180	GSM8760180: WT Replicate 2; Danio rerio; RNA Seq	GSM8760180 r1	GSM8760180	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT2_S6_L002_R1_001.fastq.gz	fastq	1150109368.0	15133018.0	GSM8760180 r2	0:76	A:272466884;C:280134047;G:274738822;T:322560009;N:209606	76		272466884	280134047	274738822	322560009	209606	SRX27491065	SRS23912863	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34644	34644	SRR32145175	SRX27491065	SRS23912863	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 2	GSM8760180	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760180	GSM8760180: WT Replicate 2; Danio rerio; RNA Seq	GSM8760180 r1	GSM8760180	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT2_S6_L003_R1_001.fastq.gz	fastq	1181538408.0	15546558.0	GSM8760180 r3	0:76	A:281618798;C:286909225;G:281700417;T:331210989;N:98979	76		281618798	286909225	281700417	331210989	98979	SRX27491065	SRS23912863	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34645	34645	SRR32145176	SRX27491065	SRS23912863	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 2	GSM8760180	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 2	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760180	GSM8760180: WT Replicate 2; Danio rerio; RNA Seq	GSM8760180 r1	GSM8760180	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT2_S6_L004_R1_001.fastq.gz	fastq	1144519796.0	15059471.0	GSM8760180 r4	0:76	A:272627373;C:278113659;G:272292478;T:321399688;N:86598	76		272627373	278113659	272292478	321399688	86598	SRX27491065	SRS23912863	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34646	34646	SRR32145177	SRX27491064	SRS23912862	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 1	GSM8760179	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760179	GSM8760179: WT Replicate 1; Danio rerio; RNA Seq	GSM8760179 r1	GSM8760179	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT1_S5_L001_R1_001.fastq.gz	fastq	1231111156.0	16198831.0	GSM8760179 r1	0:76	A:302054822;C:285868196;G:294755776;T:348218223;N:214139	76		302054822	285868196	294755776	348218223	214139	SRX27491064	SRS23912862	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34647	34647	SRR32145178	SRX27491064	SRS23912862	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 1	GSM8760179	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760179	GSM8760179: WT Replicate 1; Danio rerio; RNA Seq	GSM8760179 r1	GSM8760179	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT1_S5_L002_R1_001.fastq.gz	fastq	1182939392.0	15564992.0	GSM8760179 r2	0:76	A:289611553;C:275053581;G:283000505;T:335062758;N:210995	76		289611553	275053581	283000505	335062758	210995	SRX27491064	SRS23912862	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34648	34648	SRR32145179	SRX27491064	SRS23912862	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 1	GSM8760179	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760179	GSM8760179: WT Replicate 1; Danio rerio; RNA Seq	GSM8760179 r1	GSM8760179	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT1_S5_L003_R1_001.fastq.gz	fastq	1211221728.0	15937128.0	GSM8760179 r3	0:76	A:297941702;C:281047445;G:289384552;T:342744260;N:103769	76		297941702	281047445	289384552	342744260	103769	SRX27491064	SRS23912862	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
34649	34649	SRR32145180	SRX27491064	SRS23912862	SRP560249	PRJNA1216300	Insulin like growth factor signalling regulates zebrafish lymphatic vessel development	GSE288160	Transcriptome Analysis	RNA Seq analysis reveals that kat6a chondrocytes have reduced expression of the IGF signalling gene pappa2 Overall design: Differential gene expression analysis from RNA seq data comparing WT zebrafish chondrocytes to kat6a deficient chondrocytes in biological quadruplet.				WT Replicate 1	GSM8760179	tissue:Chondrocyte\|cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry\|geo loc name:missing\|collection date:missing	WT Replicate 1	The filtered clean reads were mapped to the Danio rerio reference genome GRCz10 by HISAT2. StringTie and the R package Ballgown were used to identify differentially expressed genes DEGs with a P value of < 0.01 Assembly: GRCz10 Supplementary files format and content: Excel file includes FPKM values for genes. Each sample S1 S8 is a separate column	Chondrocyte		At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer	Zebrafish larvae were raised in E3 medium supplemented with 0.003% PTU at 28.5 degrees.	cell type:Chondrocyte\|genotype:Tgsox10:EGFP; Tgcol2a1a:mcherry	GSM8760179	GSM8760179: WT Replicate 1; Danio rerio; RNA Seq	GSM8760179 r1	GSM8760179	1	At 3 dpf sox:10:EGFP;col2a1a:mcherry double expressing chondrocytes were isolated from whole larvae by FACS. RNA seq libraries were prepared using the Nextflex Rapid directional RNA Seq kit Perkin Elmer		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP560249		WT1_S5_L004_R1_001.fastq.gz	fastq	1173801836.0	15444761.0	GSM8760179 r4	0:76	A:288534595;C:272469282;G:279986497;T:332720262;N:91200	76		288534595	272469282	279986497	332720262	91200	SRX27491064	SRS23912862	SRA2062832	Molecular Medicine and Pathology, University of Auckland	Molecular Medicine and Pathology, University of Auckland												B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	New Zealand	2025-01-27	Larval	Larval	Bone or Cartilage	Skeletal Element
38060	38060	SRR1524244	SRX661009	SRS665984	SRP044781	PRJNA255848	Danio rerio Transcriptome	PRJNA255848	Transcriptome Analysis	Transcriptome analysis of 12 zebrafish tissues	parent bioproject:PRJNA255979	pubmed:27189481	Zebrafish Bones	Zebrafish B1s	F Dr 8	strain:AB\|age:5 month\|biomaterial provider:INRA\|sex:female\|tissue:B1s\|BioSampleModel:Model organism or animal									Zebrafish B1s	F Dr 8	F Dr 8	Total RNA was qualified using an Agilent BioAnalyzer and 1 µg was used for polyA selection and library construction with Illumina's TruSeq stranded total RNA sample preparation kit according to the manufacturer's instructions TruSeq stranded total RNA SamplePrep Guide RevC			RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000	<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>200</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>101</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>	SRP044781		F_Dr_8_ACAGTG_L003_R2.fastq.gz F_Dr_8_ACAGTG_L003_R1.fastq.gz	fastq fastq	19343193000.0	96715965.0	F Dr 8 files	0:100 1:100	A:5011655819;C:4570121318;G:4634671917;T:4933523152;N:193220794	100	100	5011655819	4570121318	4634671917	4933523152	193220794	SRX661009	SRS665984	SRA176464	INRA\|Fish Physiology and Genomics	INRA PhyloFish	2	0.88337	0.91338	0.05259	0.05508	0.75103	0.75317	0.51459	0.51744	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	poly_a	trueseq	bulk	unknown	unknown	France	2014-07-26	Adult	Adult	Bone or Cartilage	Skeletal Element
58579	58579	SRR11425295	SRX8003661	SRS6377641	SRP254053	PRJNA615232	Control of osteoblast regeneration by a train of Erk activity waves	GSE147551	Transcriptome Analysis	We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.		pubmed:33408418		high Erk activity; rep1	GSM4433141	tissue:high Erk activity\|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+\|cell type:osteoblasts of regenerating zebrafish scales	high Erk activity; rep1	Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	high Erk activity	Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424	RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01	Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube.	fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+\|cell type:osteoblasts of regenerating zebrafish scales	GSM4433141	GSM4433141: high Erk activity; rep1; Danio rerio; RNA Seq	GSM4433141		1	RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01	GEO Accession:GSM4433141	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500		SRP254053		3G_plus_1.fq.gz 3G_plus_2.fq.gz	fastq fastq	4698595200.0	46985952.0	GSM4433141 r1	0:100 1:100	A:1261622105;C:1085007643;G:1066886112;T:1285079340;N:0	100	100	1261622105	1085007643	1066886112	1285079340	0	SRX8003661	SRS6377641	SRA1059429	GEO	Poss, Cell Biology, Duke University	1	0.86576		0.11767		0.81262		0.52377		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
58580	58580	SRR11425294	SRX8003660	SRS6377640	SRP254053	PRJNA615232	Control of osteoblast regeneration by a train of Erk activity waves	GSE147551	Transcriptome Analysis	We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.		pubmed:33408418		low Erk activity; rep3	GSM4433140	tissue:low Erk activity\|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin \|cell type:osteoblasts of regenerating zebrafish scales	low Erk activity; rep3	Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	low Erk activity	Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424	RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01	Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube.	fluorescence:osx:H2A mCherry+ osx:Venus hGeminin \|cell type:osteoblasts of regenerating zebrafish scales	GSM4433140	GSM4433140: low Erk activity; rep3; Danio rerio; RNA Seq	GSM4433140		1	RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01	GEO Accession:GSM4433140	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500		SRP254053		6B_minus_1.fq.gz 6B_minus_2.fq.gz	fastq fastq	4707217000.0	47072170.0	GSM4433140 r1	0:100 1:100	A:1268188059;C:1086056259;G:1067448053;T:1285524629;N:0	100	100	1268188059	1086056259	1067448053	1285524629	0	SRX8003660	SRS6377640	SRA1059429	GEO	Poss, Cell Biology, Duke University	1	0.88883		0.05585		0.82071		0.47905		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
58581	58581	SRR11425293	SRX8003659	SRS6377639	SRP254053	PRJNA615232	Control of osteoblast regeneration by a train of Erk activity waves	GSE147551	Transcriptome Analysis	We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.		pubmed:33408418		low Erk activity; rep2	GSM4433139	tissue:low Erk activity\|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin \|cell type:osteoblasts of regenerating zebrafish scales	low Erk activity; rep2	Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	low Erk activity	Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424	RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01	Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube.	fluorescence:osx:H2A mCherry+ osx:Venus hGeminin \|cell type:osteoblasts of regenerating zebrafish scales	GSM4433139	GSM4433139: low Erk activity; rep2; Danio rerio; RNA Seq	GSM4433139		1	RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01	GEO Accession:GSM4433139	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500		SRP254053		5G_minus_1.fq.gz 5G_minus_2.fq.gz	fastq fastq	4705295600.0	47052956.0	GSM4433139 r1	0:100 1:100	A:1240779500;C:1112511484;G:1096653049;T:1255351567;N:0	100	100	1240779500	1112511484	1096653049	1255351567	0	SRX8003659	SRS6377639	SRA1059429	GEO	Poss, Cell Biology, Duke University	1	0.89254		0.04065		0.81197		0.46307		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
58582	58582	SRR11425292	SRX8003658	SRS6377638	SRP254053	PRJNA615232	Control of osteoblast regeneration by a train of Erk activity waves	GSE147551	Transcriptome Analysis	We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.		pubmed:33408418		low Erk activity; rep1	GSM4433138	tissue:low Erk activity\|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin \|cell type:osteoblasts of regenerating zebrafish scales	low Erk activity; rep1	Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	low Erk activity	Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424	RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01	Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube.	fluorescence:osx:H2A mCherry+ osx:Venus hGeminin \|cell type:osteoblasts of regenerating zebrafish scales	GSM4433138	GSM4433138: low Erk activity; rep1; Danio rerio; RNA Seq	GSM4433138		1	RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01	GEO Accession:GSM4433138	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500		SRP254053		3G_minus_1.fq.gz 3G_minus_2.fq.gz	fastq fastq	4707783400.0	47077834.0	GSM4433138 r1	0:100 1:100	A:1275040914;C:1077730597;G:1059242617;T:1295769272;N:0	100	100	1275040914	1077730597	1059242617	1295769272	0	SRX8003658	SRS6377638	SRA1059429	GEO	Poss, Cell Biology, Duke University	1	0.8629		0.13994		0.7838		0.50568		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
58583	58583	SRR11425297	SRX8003657	SRS6377637	SRP254053	PRJNA615232	Control of osteoblast regeneration by a train of Erk activity waves	GSE147551	Transcriptome Analysis	We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.		pubmed:33408418		high Erk activity; rep3	GSM4433143	tissue:high Erk activity\|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+\|cell type:osteoblasts of regenerating zebrafish scales	high Erk activity; rep3	Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	high Erk activity	Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424	RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01	Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube.	fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+\|cell type:osteoblasts of regenerating zebrafish scales	GSM4433143	GSM4433143: high Erk activity; rep3; Danio rerio; RNA Seq	GSM4433143		1	RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01	GEO Accession:GSM4433143	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500		SRP254053		6B_plus_1.fq.gz 6B_plus_2.fq.gz	fastq fastq	4703728000.0	47037280.0	GSM4433143 r1	0:100 1:100	A:1231849303;C:1116643672;G:1102072724;T:1253162301;N:0	100	100	1231849303	1116643672	1102072724	1253162301	0	SRX8003657	SRS6377637	SRA1059429	GEO	Poss, Cell Biology, Duke University	1	0.89702		0.07131		0.82978		0.49499		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
58584	58584	SRR11425296	SRX8003656	SRS6377636	SRP254053	PRJNA615232	Control of osteoblast regeneration by a train of Erk activity waves	GSE147551	Transcriptome Analysis	We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.		pubmed:33408418		high Erk activity; rep2	GSM4433142	tissue:high Erk activity\|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+\|cell type:osteoblasts of regenerating zebrafish scales	high Erk activity; rep2	Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq	high Erk activity	Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424	RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01	Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube.	fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+\|cell type:osteoblasts of regenerating zebrafish scales	GSM4433142	GSM4433142: high Erk activity; rep2; Danio rerio; RNA Seq	GSM4433142		1	RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01	GEO Accession:GSM4433142	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	BGISEQ	BGISEQ-500		SRP254053		5G_plus_1.fq.gz 5G_plus_2.fq.gz	fastq fastq	4708623600.0	47086236.0	GSM4433142 r1	0:100 1:100	A:1200601624;C:1150903127;G:1136628277;T:1220490572;N:0	100	100	1200601624	1150903127	1136628277	1220490572	0	SRX8003656	SRS6377636	SRA1059429	GEO	Poss, Cell Biology, Duke University	1	0.90729		0.03751		0.84433		0.50342		100		B		usable mapping rate	bgi	bgi	unknown	cdna_unspecified	unknown	bulk	unknown	unknown	United States	2020-03-25	Undetermined	Undetermined	Bone or Cartilage	Skeletal Element
76931	76931	SRR25386906	SRX21125096	SRS18391094	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR2a 4dpf osteoblasts P2 rep 1	GSM7656643	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR2a 4dpf osteoblasts P2 rep 1	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656643	GSM7656643: RR2a 4dpf osteoblasts P2 rep 1; Danio rerio; RNA Seq	GSM7656643 r1	GSM7656643	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR2a-P2_NGS20-O032_HGLCNBGXG_S1_L003_R1_001.fastq.gz	fastq	373177684.0	5548694.0	GSM7656643 r3	0:67.26	A:100760112;C:81480585;G:85122648;T:102415267;N:3399072	67		100760112	81480585	85122648	102415267	3399072	SRX21125096	SRS18391094	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.8728		0.31033		0.8072		0.60657		68		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76932	76932	SRR25386907	SRX21125096	SRS18391094	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR2a 4dpf osteoblasts P2 rep 1	GSM7656643	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR2a 4dpf osteoblasts P2 rep 1	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656643	GSM7656643: RR2a 4dpf osteoblasts P2 rep 1; Danio rerio; RNA Seq	GSM7656643 r1	GSM7656643	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR2a-P2_NGS20-O032_HGLCNBGXG_S1_L004_R1_001.fastq.gz	fastq	373962152.0	5557214.0	GSM7656643 r4	0:67.29	A:100972761;C:81555058;G:85226241;T:102843430;N:3364662	67		100972761	81555058	85226241	102843430	3364662	SRX21125096	SRS18391094	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.8736		0.31177		0.80667		0.59856		70		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76933	76933	SRR25386924	SRX21125096	SRS18391094	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR2a 4dpf osteoblasts P2 rep 1	GSM7656643	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR2a 4dpf osteoblasts P2 rep 1	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656643	GSM7656643: RR2a 4dpf osteoblasts P2 rep 1; Danio rerio; RNA Seq	GSM7656643 r1	GSM7656643	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR2a-P2_NGS20-O032_HGLCNBGXG_S1_L001_R1_001.fastq.gz	fastq	373269811.0	5548624.0	GSM7656643 r1	0:67.27	A:101075219;C:81326431;G:85043234;T:102437099;N:3387828	67		101075219	81326431	85043234	102437099	3387828	SRX21125096	SRS18391094	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.87208		0.30902		0.80923		0.62143		41		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76934	76934	SRR25386925	SRX21125096	SRS18391094	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR2a 4dpf osteoblasts P2 rep 1	GSM7656643	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR2a 4dpf osteoblasts P2 rep 1	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656643	GSM7656643: RR2a 4dpf osteoblasts P2 rep 1; Danio rerio; RNA Seq	GSM7656643 r1	GSM7656643	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR2a-P2_NGS20-O032_HGLCNBGXG_S1_L002_R1_001.fastq.gz	fastq	362918448.0	5391108.0	GSM7656643 r2	0:67.32	A:98186136;C:79161985;G:82672936;T:99657172;N:3240219	67		98186136	79161985	82672936	99657172	3240219	SRX21125096	SRS18391094	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.8708		0.30958		0.80775		0.60608		74		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76935	76935	SRR25386908	SRX21125095	SRS18391093	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR6a 4dpf osteoblasts P2 rep 4	GSM7656645	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR6a 4dpf osteoblasts P2 rep 4	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656645	GSM7656645: RR6a 4dpf osteoblasts P2 rep 4; Danio rerio; RNA Seq	GSM7656645 r1	GSM7656645	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR6a-P2_NGS20-O037_HGLCNBGXG_S6_L001_R1_001.fastq.gz	fastq	354032873.0	4986287.0	GSM7656645 r1	0:71.00	A:94144867;C:80102104;G:82817752;T:95495724;N:1472426	71		94144867	80102104	82817752	95495724	1472426	SRX21125095	SRS18391093	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.89937		0.33561		0.78624		0.59931		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76936	76936	SRR25386909	SRX21125095	SRS18391093	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR6a 4dpf osteoblasts P2 rep 4	GSM7656645	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR6a 4dpf osteoblasts P2 rep 4	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656645	GSM7656645: RR6a 4dpf osteoblasts P2 rep 4; Danio rerio; RNA Seq	GSM7656645 r1	GSM7656645	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR6a-P2_NGS20-O037_HGLCNBGXG_S6_L002_R1_001.fastq.gz	fastq	346361358.0	4874773.0	GSM7656645 r2	0:71.05	A:92065302;C:78397028;G:81045788;T:93453382;N:1399858	71		92065302	78397028	81045788	93453382	1399858	SRX21125095	SRS18391093	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.90158		0.33472		0.78553		0.5992		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76937	76937	SRR25386910	SRX21125095	SRS18391093	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR6a 4dpf osteoblasts P2 rep 4	GSM7656645	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR6a 4dpf osteoblasts P2 rep 4	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656645	GSM7656645: RR6a 4dpf osteoblasts P2 rep 4; Danio rerio; RNA Seq	GSM7656645 r1	GSM7656645	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR6a-P2_NGS20-O037_HGLCNBGXG_S6_L003_R1_001.fastq.gz	fastq	355035161.0	5000095.0	GSM7656645 r3	0:71.01	A:94319592;C:80407508;G:83110050;T:95730889;N:1467122	71		94319592	80407508	83110050	95730889	1467122	SRX21125095	SRS18391093	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.90115		0.33357		0.78675		0.57285		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76938	76938	SRR25386911	SRX21125095	SRS18391093	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR6a 4dpf osteoblasts P2 rep 4	GSM7656645	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR6a 4dpf osteoblasts P2 rep 4	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656645	GSM7656645: RR6a 4dpf osteoblasts P2 rep 4; Danio rerio; RNA Seq	GSM7656645 r1	GSM7656645	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR6a-P2_NGS20-O037_HGLCNBGXG_S6_L004_R1_001.fastq.gz	fastq	356149314.0	5014069.0	GSM7656645 r4	0:71.03	A:94655529;C:80576651;G:83343452;T:96095982;N:1477700	71		94655529	80576651	83343452	96095982	1477700	SRX21125095	SRS18391093	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.90138		0.33348		0.78455		0.5911		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76939	76939	SRR25386912	SRX21125094	SRS18391092	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR3a 4dpf osteoblasts P2 rep 2	GSM7656644	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR3a 4dpf osteoblasts P2 rep 2	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656644	GSM7656644: RR3a 4dpf osteoblasts P2 rep 2; Danio rerio; RNA Seq	GSM7656644 r1	GSM7656644	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR3a-P2_NGS20-O034_HGLCNBGXG_S3_L001_R1_001.fastq.gz	fastq	338589143.0	4761586.0	GSM7656644 r1	0:71.11	A:97196593;C:69615487;G:71880789;T:98743111;N:1153163	71		97196593	69615487	71880789	98743111	1153163	SRX21125094	SRS18391092	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.8916		0.25165		0.77244		0.58676		76		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76940	76940	SRR25386913	SRX21125094	SRS18391092	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR3a 4dpf osteoblasts P2 rep 2	GSM7656644	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR3a 4dpf osteoblasts P2 rep 2	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656644	GSM7656644: RR3a 4dpf osteoblasts P2 rep 2; Danio rerio; RNA Seq	GSM7656644 r1	GSM7656644	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR3a-P2_NGS20-O034_HGLCNBGXG_S3_L002_R1_001.fastq.gz	fastq	331811774.0	4663625.0	GSM7656644 r2	0:71.15	A:95222586;C:68212365;G:70454008;T:96805245;N:1117570	71		95222586	68212365	70454008	96805245	1117570	SRX21125094	SRS18391092	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.89276		0.25194		0.7698		0.58851		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76941	76941	SRR25386914	SRX21125094	SRS18391092	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR3a 4dpf osteoblasts P2 rep 2	GSM7656644	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR3a 4dpf osteoblasts P2 rep 2	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656644	GSM7656644: RR3a 4dpf osteoblasts P2 rep 2; Danio rerio; RNA Seq	GSM7656644 r1	GSM7656644	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR3a-P2_NGS20-O034_HGLCNBGXG_S3_L003_R1_001.fastq.gz	fastq	339208892.0	4771033.0	GSM7656644 r3	0:71.10	A:97276491;C:69781643;G:72044207;T:98948884;N:1157667	71		97276491	69781643	72044207	98948884	1157667	SRX21125094	SRS18391092	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.89219		0.2516		0.77102		0.58563		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76942	76942	SRR25386915	SRX21125094	SRS18391092	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR3a 4dpf osteoblasts P2 rep 2	GSM7656644	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR3a 4dpf osteoblasts P2 rep 2	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:high P2 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656644	GSM7656644: RR3a 4dpf osteoblasts P2 rep 2; Danio rerio; RNA Seq	GSM7656644 r1	GSM7656644	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR3a-P2_NGS20-O034_HGLCNBGXG_S3_L004_R1_001.fastq.gz	fastq	341114353.0	4796386.0	GSM7656644 r4	0:71.12	A:97859710;C:70136066;G:72385473;T:99567064;N:1166040	71		97859710	70136066	72385473	99567064	1166040	SRX21125094	SRS18391092	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.89236		0.25322		0.77189		0.58747		46		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76943	76943	SRR25386916	SRX21125093	SRS18391091	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR8b 4dpf osteoblasts P1 rep 6	GSM7656642	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR8b 4dpf osteoblasts P1 rep 6	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656642	GSM7656642: RR8b 4dpf osteoblasts P1 rep 6; Danio rerio; RNA Seq	GSM7656642 r1	GSM7656642	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR8b-P1_NGS20-O039_HGLCNBGXG_S8_L001_R1_001.fastq.gz	fastq	330198165.0	4722206.0	GSM7656642 r1	0:69.92	A:93808782;C:67002978;G:70951394;T:96805500;N:1629511	69		93808782	67002978	70951394	96805500	1629511	SRX21125093	SRS18391091	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.85804		0.25861		0.77918		0.66339		76		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76944	76944	SRR25386917	SRX21125093	SRS18391091	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR8b 4dpf osteoblasts P1 rep 6	GSM7656642	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR8b 4dpf osteoblasts P1 rep 6	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656642	GSM7656642: RR8b 4dpf osteoblasts P1 rep 6; Danio rerio; RNA Seq	GSM7656642 r1	GSM7656642	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR8b-P1_NGS20-O039_HGLCNBGXG_S8_L002_R1_001.fastq.gz	fastq	319742147.0	4570291.0	GSM7656642 r2	0:69.96	A:90789631;C:65040424;G:68780271;T:93589780;N:1542041	69		90789631	65040424	68780271	93589780	1542041	SRX21125093	SRS18391091	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.8599		0.25985		0.7805		0.6659		74		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76945	76945	SRR25386918	SRX21125093	SRS18391091	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR8b 4dpf osteoblasts P1 rep 6	GSM7656642	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR8b 4dpf osteoblasts P1 rep 6	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656642	GSM7656642: RR8b 4dpf osteoblasts P1 rep 6; Danio rerio; RNA Seq	GSM7656642 r1	GSM7656642	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR8b-P1_NGS20-O039_HGLCNBGXG_S8_L003_R1_001.fastq.gz	fastq	328154548.0	4693975.0	GSM7656642 r3	0:69.91	A:93075572;C:66836894;G:70660521;T:95966166;N:1615395	69		93075572	66836894	70660521	95966166	1615395	SRX21125093	SRS18391091	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.85887		0.2556		0.77707		0.66048		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76946	76946	SRR25386919	SRX21125093	SRS18391091	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR8b 4dpf osteoblasts P1 rep 6	GSM7656642	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR8b 4dpf osteoblasts P1 rep 6	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656642	GSM7656642: RR8b 4dpf osteoblasts P1 rep 6; Danio rerio; RNA Seq	GSM7656642 r1	GSM7656642	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR8b-P1_NGS20-O039_HGLCNBGXG_S8_L004_R1_001.fastq.gz	fastq	329194766.0	4707630.0	GSM7656642 r4	0:69.93	A:93301373;C:67002800;G:70828695;T:96461490;N:1600408	69		93301373	67002800	70828695	96461490	1600408	SRX21125093	SRS18391091	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.86031		0.25799		0.77997		0.66228		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76947	76947	SRR25386920	SRX21125092	SRS18391090	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR7b 4dpf osteoblasts P1 rep 5	GSM7656641	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR7b 4dpf osteoblasts P1 rep 5	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656641	GSM7656641: RR7b 4dpf osteoblasts P1 rep 5; Danio rerio; RNA Seq	GSM7656641 r1	GSM7656641	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR7b-P1_NGS20-O038_HGLCNBGXG_S7_L001_R1_001.fastq.gz	fastq	351643397.0	4968808.0	GSM7656641 r1	0:70.77	A:105100153;C:66835699;G:69586761;T:108735482;N:1385302	70		105100153	66835699	69586761	108735482	1385302	SRX21125092	SRS18391090	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.86068		0.33407		0.74511		0.6177		76		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76948	76948	SRR25386921	SRX21125092	SRS18391090	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR7b 4dpf osteoblasts P1 rep 5	GSM7656641	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR7b 4dpf osteoblasts P1 rep 5	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656641	GSM7656641: RR7b 4dpf osteoblasts P1 rep 5; Danio rerio; RNA Seq	GSM7656641 r1	GSM7656641	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR7b-P1_NGS20-O038_HGLCNBGXG_S7_L002_R1_001.fastq.gz	fastq	343842500.0	4855139.0	GSM7656641 r2	0:70.82	A:102704108;C:65392360;G:68061878;T:106355606;N:1328548	70		102704108	65392360	68061878	106355606	1328548	SRX21125092	SRS18391090	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.8638		0.3363		0.74326		0.61886		76		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76949	76949	SRR25386922	SRX21125092	SRS18391090	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR7b 4dpf osteoblasts P1 rep 5	GSM7656641	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR7b 4dpf osteoblasts P1 rep 5	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656641	GSM7656641: RR7b 4dpf osteoblasts P1 rep 5; Danio rerio; RNA Seq	GSM7656641 r1	GSM7656641	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR7b-P1_NGS20-O038_HGLCNBGXG_S7_L003_R1_001.fastq.gz	fastq	351976151.0	4973882.0	GSM7656641 r3	0:70.76	A:105062432;C:66994989;G:69682303;T:108860965;N:1375462	70		105062432	66994989	69682303	108860965	1375462	SRX21125092	SRS18391090	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.86197		0.33599		0.7404		0.62359		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76950	76950	SRR25386923	SRX21125092	SRS18391090	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR7b 4dpf osteoblasts P1 rep 5	GSM7656641	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR7b 4dpf osteoblasts P1 rep 5	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656641	GSM7656641: RR7b 4dpf osteoblasts P1 rep 5; Danio rerio; RNA Seq	GSM7656641 r1	GSM7656641	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR7b-P1_NGS20-O038_HGLCNBGXG_S7_L004_R1_001.fastq.gz	fastq	353874367.0	4998321.0	GSM7656641 r4	0:70.80	A:105642560;C:67318464;G:70033014;T:109504559;N:1375770	70		105642560	67318464	70033014	109504559	1375770	SRX21125092	SRS18391090	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.86207		0.33692		0.74105		0.61979		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76951	76951	SRR25386926	SRX21125091	SRS18391089	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR4b 4dpf osteoblasts P1 rep 3	GSM7656640	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR4b 4dpf osteoblasts P1 rep 3	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656640	GSM7656640: RR4b 4dpf osteoblasts P1 rep 3; Danio rerio; RNA Seq	GSM7656640 r1	GSM7656640	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR4b-P1_NGS20-O036_HGLCNBGXG_S5_L001_R1_001.fastq.gz	fastq	402745635.0	5793956.0	GSM7656640 r1	0:69.51	A:116205887;C:79952535;G:84359294;T:120217077;N:2010842	69		116205887	79952535	84359294	120217077	2010842	SRX21125091	SRS18391089	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.86267		0.24591		0.7654		0.63731		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76952	76952	SRR25386927	SRX21125091	SRS18391089	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR4b 4dpf osteoblasts P1 rep 3	GSM7656640	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR4b 4dpf osteoblasts P1 rep 3	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656640	GSM7656640: RR4b 4dpf osteoblasts P1 rep 3; Danio rerio; RNA Seq	GSM7656640 r1	GSM7656640	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR4b-P1_NGS20-O036_HGLCNBGXG_S5_L002_R1_001.fastq.gz	fastq	390449256.0	5611210.0	GSM7656640 r2	0:69.58	A:112541261;C:77603748;G:81768732;T:116665670;N:1869845	69		112541261	77603748	81768732	116665670	1869845	SRX21125091	SRS18391089	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.86222		0.24746		0.7681		0.64011		60		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76953	76953	SRR25386928	SRX21125091	SRS18391089	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR4b 4dpf osteoblasts P1 rep 3	GSM7656640	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR4b 4dpf osteoblasts P1 rep 3	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656640	GSM7656640: RR4b 4dpf osteoblasts P1 rep 3; Danio rerio; RNA Seq	GSM7656640 r1	GSM7656640	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR4b-P1_NGS20-O036_HGLCNBGXG_S5_L003_R1_001.fastq.gz	fastq	402308010.0	5787745.0	GSM7656640 r3	0:69.51	A:115787104;C:80048838;G:84391496;T:120095088;N:1985484	69		115787104	80048838	84391496	120095088	1985484	SRX21125091	SRS18391089	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.86229		0.24527		0.76619		0.64409		50		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76954	76954	SRR25386929	SRX21125091	SRS18391089	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR4b 4dpf osteoblasts P1 rep 3	GSM7656640	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR4b 4dpf osteoblasts P1 rep 3	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656640	GSM7656640: RR4b 4dpf osteoblasts P1 rep 3; Danio rerio; RNA Seq	GSM7656640 r1	GSM7656640	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR4b-P1_NGS20-O036_HGLCNBGXG_S5_L004_R1_001.fastq.gz	fastq	401717863.0	5776032.0	GSM7656640 r4	0:69.55	A:115579821;C:79871913;G:84153308;T:120146558;N:1966263	69		115579821	79871913	84153308	120146558	1966263	SRX21125091	SRS18391089	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.86513		0.24776		0.76493		0.64344		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76955	76955	SRR25386930	SRX21125090	SRS18391088	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR3b 4dpf osteoblasts P1 rep 2	GSM7656639	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR3b 4dpf osteoblasts P1 rep 2	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656639	GSM7656639: RR3b 4dpf osteoblasts P1 rep 2; Danio rerio; RNA Seq	GSM7656639 r1	GSM7656639	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR3b-P1_NGS20-O035_HGLCNBGXG_S4_L001_R1_001.fastq.gz	fastq	429035205.0	6206744.0	GSM7656639 r1	0:69.12	A:120492165;C:90539580;G:93847354;T:121771690;N:2384416	69		120492165	90539580	93847354	121771690	2384416	SRX21125090	SRS18391088	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.88814		0.2441		0.75605		0.59921		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76956	76956	SRR25386931	SRX21125090	SRS18391088	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR3b 4dpf osteoblasts P1 rep 2	GSM7656639	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR3b 4dpf osteoblasts P1 rep 2	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656639	GSM7656639: RR3b 4dpf osteoblasts P1 rep 2; Danio rerio; RNA Seq	GSM7656639 r1	GSM7656639	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR3b-P1_NGS20-O035_HGLCNBGXG_S4_L002_R1_001.fastq.gz	fastq	415751420.0	6007024.0	GSM7656639 r2	0:69.21	A:116706448;C:87823404;G:90986248;T:118009974;N:2225346	69		116706448	87823404	90986248	118009974	2225346	SRX21125090	SRS18391088	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.88959		0.24483		0.7531		0.60005		76		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76957	76957	SRR25386932	SRX21125090	SRS18391088	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR3b 4dpf osteoblasts P1 rep 2	GSM7656639	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR3b 4dpf osteoblasts P1 rep 2	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656639	GSM7656639: RR3b 4dpf osteoblasts P1 rep 2; Danio rerio; RNA Seq	GSM7656639 r1	GSM7656639	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR3b-P1_NGS20-O035_HGLCNBGXG_S4_L003_R1_001.fastq.gz	fastq	429244072.0	6207840.0	GSM7656639 r3	0:69.15	A:120352313;C:90741598;G:94022493;T:121790485;N:2337183	69		120352313	90741598	94022493	121790485	2337183	SRX21125090	SRS18391088	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.88854		0.24321		0.75355		0.60633		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76958	76958	SRR25386933	SRX21125090	SRS18391088	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR3b 4dpf osteoblasts P1 rep 2	GSM7656639	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR3b 4dpf osteoblasts P1 rep 2	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656639	GSM7656639: RR3b 4dpf osteoblasts P1 rep 2; Danio rerio; RNA Seq	GSM7656639 r1	GSM7656639	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR3b-P1_NGS20-O035_HGLCNBGXG_S4_L004_R1_001.fastq.gz	fastq	427969591.0	6187997.0	GSM7656639 r4	0:69.16	A:120010443;C:90373192;G:93656303;T:121564988;N:2364665	69		120010443	90373192	93656303	121564988	2364665	SRX21125090	SRS18391088	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.88877		0.24406		0.75383		0.61019		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76959	76959	SRR25386934	SRX21125089	SRS18391087	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR2b 4dpf osteoblasts P1 rep 1	GSM7656638	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR2b 4dpf osteoblasts P1 rep 1	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656638	GSM7656638: RR2b 4dpf osteoblasts P1 rep 1; Danio rerio; RNA Seq	GSM7656638 r1	GSM7656638	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR2b-P1_NGS20-O033_HGLCNBGXG_S2_L001_R1_001.fastq.gz	fastq	317336901.0	4462492.0	GSM7656638 r1	0:71.11	A:92227525;C:63104195;G:65535255;T:95288295;N:1181631	71		92227525	63104195	65535255	95288295	1181631	SRX21125089	SRS18391087	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.8761		0.23251		0.77047		0.56736		76		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76960	76960	SRR25386935	SRX21125089	SRS18391087	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR2b 4dpf osteoblasts P1 rep 1	GSM7656638	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR2b 4dpf osteoblasts P1 rep 1	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656638	GSM7656638: RR2b 4dpf osteoblasts P1 rep 1; Danio rerio; RNA Seq	GSM7656638 r1	GSM7656638	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR2b-P1_NGS20-O033_HGLCNBGXG_S2_L002_R1_001.fastq.gz	fastq	310847956.0	4367375.0	GSM7656638 r2	0:71.18	A:90294814;C:61828186;G:64235903;T:93370219;N:1118834	71		90294814	61828186	64235903	93370219	1118834	SRX21125089	SRS18391087	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.87507		0.2317		0.77137		0.5794		74		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76961	76961	SRR25386936	SRX21125089	SRS18391087	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR2b 4dpf osteoblasts P1 rep 1	GSM7656638	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR2b 4dpf osteoblasts P1 rep 1	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656638	GSM7656638: RR2b 4dpf osteoblasts P1 rep 1; Danio rerio; RNA Seq	GSM7656638 r1	GSM7656638	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR2b-P1_NGS20-O033_HGLCNBGXG_S2_L003_R1_001.fastq.gz	fastq	317967922.0	4471419.0	GSM7656638 r3	0:71.11	A:92323173;C:63305532;G:65719680;T:95440373;N:1179164	71		92323173	63305532	65719680	95440373	1179164	SRX21125089	SRS18391087	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.87563		0.23003		0.76956		0.60039		76		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element
76962	76962	SRR25386937	SRX21125089	SRS18391087	SRP450794	PRJNA997263	Osteoblasts isolated from sp7 GFP transgenics by FACS sorting of 4dpf zebrafish larvae	GSE237934	Transcriptome Analysis	The transgenic zebrafish line Tgsp7:sp7 GFP ulg071 Tg was used to obtain fluorescent cells through FACS sorting. Two populations were identifed: P1 displaying low fluorescence P2 displaying high fluorescence. Cells were collected and sumitted to RNA Seq Overall design: A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. Two populations with low P1 and high P2 fluorescence were separated. The collected cells from populations P1 and P2 about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing while libraries were prepared using the Nextera XT DNA library kit. Third party re analysis: Table P2 Sanger P1 Sanger P1 P2.csv our DESeq2 analysis of P1 and P2 4dpf larvae populations with Sanger dataset from Bioproject PRJEB7244 : ID;gene;baseMean P2 Sanger;log2FoldChange P2 Sanger;padj P2 Sanger;Sanger baseMean;P2 baseMean;ID;gene;baseMean P1 Sanger;log2FoldChange P1 Sanger;padj P1 Sanger;Sanger baseMean;P1 baseMean;ID;gene;baseMean;log2FoldChange P1 P2;padj P1 P2;P2 baseMean;P1 baseMean. Table Counts P1 P2 Sanger.csv the counts table complete with the Sanger data.				RR2b 4dpf osteoblasts P1 rep 1	GSM7656638	tissue:4dpf osteoblasts\|cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS\|geo loc name:missing\|collection date:missing	RR2b 4dpf osteoblasts P1 rep 1	The sequencing reads were processed through the Nf core rnaseq pipeline 3.0 Ewels P. A. et al. Nat Biotechnol 2020 38 3 276 278 with default parameters and using the zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 www.ensembl.org. Differential gene expression analysis was performed using DESeq2 pipeline Assembly: zebrafish reference genome GRCz11 and the annotation set from Ensembl release 103 Supplementary files format and content: Osteo Table P2/P1.csv containing: Ensembl gene ID gene name baseMean log2FoldChange lfcSE stat pvalue padj P2 baseMean P1 baseMean Supplementary files format and content: Osteo Table Counts P1 P2.csv: individual sample count files. Ensembl gene ID Gene name RR6a P2 RR8b P1 RR3a P2 RR4b P1 RR3b P1 RR2b P1 RR2a P2 RR7b P1	4dpf osteoblasts	A Tgsp7:sp7 GFP heterozygous transgenic parent was outcrossed with a wt parent to obtain a clutch of transgenic and non transgenic offspring. At 3dpf the Tg positive larvae were separated from their Tg negative siblings and raised separately in two different plates. At 4 dpf around 100 150 larvae were euthanized and transferred to gentleMACS™ C tubes Miltenyi Biotec Leiden Netherlandsin an excess of E3 medium. The supernatant was removed and replaced with 1ml to 1 5 ml of De yolk buffer prepared in house. The larvae were de yolked by vigorously pipetting up and down several times for 10 minutes and the supernatant discarded. The larvae were washed twice with HBSS buffer without xxx+2 and Mg+2 ions and phenol red free and the supernatant was discarded. The larvae are resuspended in 1 5ml digestion buffer at 28º C dissociation was performed running the protocols m brain 01 and m brain 03 according to the manufacturer's instructions in the Neural Tissue Dissociation Kit T 130 093 231 once on a gentleMACS™ Dissociator machine Miltenyi Biotec Leiden Netherlands followed by three runs of m brain 03 2 runs of protocol m brain 02 five runs of m brain 03 each run separated by continuous shaking in the water bath at 28ºC for 5 min. Then m brain 01 protocol was run before adding 30ul of Enzyme A as supplied by Miltenyi Biotec Neural Tissue Dissociation Kit T 130 093 231 followed by 4 additional runs of the m brain 03 protocol separated by 5 min incubation at 28ºC with continuous shaking and the tube transferred on ice. The samples were centrifuged at 4º C at 300g for 10 min and the supernatant discarded as gently as possible to avoid cell resuspension. The pellet was very quickly resuspended in 1ml HBSS buffer and filtered through mesh to eliminate cell clumps and aggregates. The filtered cells were collected in polypropylene tubes and viability dye 10% v/v propidium iodide Fisher Scientific Merelbeek Belgium was added to distinguish live cells from dead cells /cell debris while sorting. It is very important…	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.	Zebrafish Danio rerio of the AB strain transgenic line ulg071 Tg were obtained from breeding facilities at the GIGA Institute Liege Belgium. The water characteristics were as follows: pH = 7.4 and temperature = 28°C. The lighting was 14/10 h light/dark. Embryos were used and staged as described [28 29]. Fish were mated and spawning was stimulated by the onset of light. The day before breeding adult male and female zebrafish were set up in several breeding tanks separated by a clear plastic wall. post the light was turned on the next morning walls are removed and eggs are generated by natural mating and then collected from 30 minutes to 2 hours post spawning. post sorting fertilized clean eggs are moved to Petri dishes and incubated at 28°C in E3 medium 5 mM Na Cl 0.17 mM KCl 0.33 mM CaCl2 0.33 mM MgSO4 0.00001% Methylene Blue. The age of the embryos and larvae is indicated as hpf	cell type:4dpf osteoblasts\|cell population:low P1 fluorescence\|genotype:ulg071 Tg\|treatment:FACS	GSM7656638	GSM7656638: RR2b 4dpf osteoblasts P1 rep 1; Danio rerio; RNA Seq	GSM7656638 r1	GSM7656638	1	Cells coming from cell sorting about 30 50000 cells were immediately lysed in 0.5% Triton X 100 containing 2U/µl RNAsin and stored at 80°C. cDNAs were prepared from these lysed cells according to the SMART Seq 2.0 protocol Illumina San Diego CA USA for low input RNA sequencing. Libraries were prepared using the Nextera XT DNA library kit Ma X. Y. W. Wang M. Q. Zhang and A. F. Gazdar 2013. "DNA methylation data analysis and its application to cancer research." Epigenomics 53: 301 316.		RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	Illumina NovaSeq 6000		SRP450794	loader:fastq load.py	RR2b-P1_NGS20-O033_HGLCNBGXG_S2_L004_R1_001.fastq.gz	fastq	319113403.0	4486135.0	GSM7656638 r4	0:71.13	A:92635644;C:63461440;G:65928563;T:95917731;N:1170025	71		92635644	63461440	65928563	95917731	1170025	SRX21125089	SRS18391087	SRA1677548	Organogenesis and Regeneration, Life Sciences, Université de Liège	Organogenesis and Regeneration, Life Sciences, Université de Liège	1	0.87552		0.23103		0.76891		0.58811		75		B		usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	nextera	bulk	unknown	unknown	Belgium	2023-07-21	Multi-stage	Multi-stage	Bone or Cartilage	Skeletal Element

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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");;