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.centername,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.title,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.r3_length,run.r4_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,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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,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
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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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,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 to ensure that the steps following centrifugation are carried out by placing the tubes on ice. The cells were then brought to the FACS AriaIII sorter P18100055 and the green fluorescent cells are sorted into a 1 5 ml Eppendorf tube containing 500 ul of PBS buffer with RNAsin and 1% BSA. Note that a preliminary run was performed using the non transgenic siblings to ensure that the GFP positive cells were truly due to transgene expression  not to autofluorescence.  De yolk buffer 4ml:  44µl NaCl 5M  14.4µl KCl 0.5M  5µl NaHCO3 1M  Bidistillated water to make it up to 4ml.    Dissection buffer 4ml:  1x HBSS  buffer without xxx+2 and Mg+2 ions and phenol red free  10mM HEPES 0.5%  2mM EDTA  1% BSA  Filter using 0 22µm filter and store at 4ºC.    Digestion buffer 2ml:  1 8 ml filtered Dissection buffer   200µl TrypLeTM Select 10x Thermo Fisher Scientific  Merelbeke  Belgium  10µl Proteinase K 20µg/µl Thermo Fisher Scientific  Merelbeke  Belgium  10µl Collagenase 2 20mg/ml Thermo Fisher Scientific  Merelbeke  Belgium,"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