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 58579,SRR11425295,SRX8003661,SRS6377641,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.,,pubmed:33408418,,high Erk activity; rep1,GSM4433141,,tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,high Erk activity; rep1,Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,high Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,GSM4433141,GSM4433141: high Erk activity; rep1; Danio rerio; RNA Seq,GSM4433141,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433141,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,3G_plus_1.fq.gz 3G_plus_2.fq.gz,fastq fastq,4698595200.0,46985952.0,GSM4433141 r1,0:100 1:100,A:1261622105;C:1085007643;G:1066886112;T:1285079340;N:0,100,100,,,1261622105,1085007643,1066886112,1285079340,0,SRX8003661,SRS6377641,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.86576,,0.11767,,0.81262,,0.52377,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element 58580,SRR11425294,SRX8003660,SRS6377640,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.,,pubmed:33408418,,low Erk activity; rep3,GSM4433140,,tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,low Erk activity; rep3,Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,low Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,GSM4433140,GSM4433140: low Erk activity; rep3; Danio rerio; RNA Seq,GSM4433140,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433140,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,6B_minus_1.fq.gz 6B_minus_2.fq.gz,fastq fastq,4707217000.0,47072170.0,GSM4433140 r1,0:100 1:100,A:1268188059;C:1086056259;G:1067448053;T:1285524629;N:0,100,100,,,1268188059,1086056259,1067448053,1285524629,0,SRX8003660,SRS6377640,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.88883,,0.05585,,0.82071,,0.47905,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element 58581,SRR11425293,SRX8003659,SRS6377639,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.,,pubmed:33408418,,low Erk activity; rep2,GSM4433139,,tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,low Erk activity; rep2,Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,low Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,GSM4433139,GSM4433139: low Erk activity; rep2; Danio rerio; RNA Seq,GSM4433139,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433139,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,5G_minus_1.fq.gz 5G_minus_2.fq.gz,fastq fastq,4705295600.0,47052956.0,GSM4433139 r1,0:100 1:100,A:1240779500;C:1112511484;G:1096653049;T:1255351567;N:0,100,100,,,1240779500,1112511484,1096653049,1255351567,0,SRX8003659,SRS6377639,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.89254,,0.04065,,0.81197,,0.46307,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element 58582,SRR11425292,SRX8003658,SRS6377638,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.,,pubmed:33408418,,low Erk activity; rep1,GSM4433138,,tissue:low Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,low Erk activity; rep1,Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,low Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin |cell type:osteoblasts of regenerating zebrafish scales,GSM4433138,GSM4433138: low Erk activity; rep1; Danio rerio; RNA Seq,GSM4433138,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433138,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,3G_minus_1.fq.gz 3G_minus_2.fq.gz,fastq fastq,4707783400.0,47077834.0,GSM4433138 r1,0:100 1:100,A:1275040914;C:1077730597;G:1059242617;T:1295769272;N:0,100,100,,,1275040914,1077730597,1059242617,1295769272,0,SRX8003658,SRS6377638,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.8629,,0.13994,,0.7838,,0.50568,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element 58583,SRR11425297,SRX8003657,SRS6377637,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.,,pubmed:33408418,,high Erk activity; rep3,GSM4433143,,tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,high Erk activity; rep3,Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,high Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,GSM4433143,GSM4433143: high Erk activity; rep3; Danio rerio; RNA Seq,GSM4433143,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433143,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,6B_plus_1.fq.gz 6B_plus_2.fq.gz,fastq fastq,4703728000.0,47037280.0,GSM4433143 r1,0:100 1:100,A:1231849303;C:1116643672;G:1102072724;T:1253162301;N:0,100,100,,,1231849303,1116643672,1102072724,1253162301,0,SRX8003657,SRS6377637,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.89702,,0.07131,,0.82978,,0.49499,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element 58584,SRR11425296,SRX8003656,SRS6377636,SRP254053,PRJNA615232,Control of osteoblast regeneration by a train of Erk activity waves,GSE147551,Transcriptome Analysis,We report here a dataset regarding the transcriptome of Erk active osteoblasts in regenerating zebrafish scales. We recently discovered that the marker osx:Venus hGeminin anti correlates with Erk activity in those cells. Thus by sorting using FACS cells based on both the expression of an osteoblast marker osx::H2A mCherry and the levels of hGeminin we could sort osteoblasts into separate Erk+ and Erk populations and perform RNAsequence in triplicates. We found that dusp and sprouty transcripts are elevated in osteoblasts with high Erk activity. Specifically dusp2 dusp5 and spry4 transcripts are predominant in scales and consistently present at higher levels in the population enriched for Erk+ cells. Overall design: Comparison of the transcriptome of osteoblasts of regenerating zebrafish scales with high and low Erk activity. Cells are sorted on the basis of their osx:Venus hGeminin signal which anti correlates with Erk activity.,,pubmed:33408418,,high Erk activity; rep2,GSM4433142,,tissue:high Erk activity|fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,high Erk activity; rep2,Reads were trimmed by Trim Galore 0.4.1 with q 15 paired and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq annotation. Gene level read counts were obtained using the featureCounts v1.6.1 by the reads with MAPQ greater than 30 Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq,high Erk activity,Cells were analyzed and sorted using a SH800S Sony Cell Sorter using a 100 µm disposable chip. Initially events were gated using Forward versus Side Scatter Areas 488 nm laser. Then single cells were enriched by gating Forward Scatter Height versus Forward Scatter Area 488 nm excitation laser. Live cells were enriched by selecting a population with low DAPI emission 405 nm excitation laser. Finally H2A mCherry+ Venus hGeminin and H2A mCherry+ Venus hGeminin+ were sorted by gating Venus hGeminin 488 nm excitation laser versus mCherry 561 nm excitation laser. Cells were collected in PBS or TriReagent Sigma T9424,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,Scale regeneration was induced by plucking about 50 scales in three rows from each side of osx:H2A mCherry osx:Venus hGeminin fish. At 4 days post plucking dpp all regenerating scales were plucked and collected in PBS on ice. About 3 5 fish were used per sample. Tissue was pelleted by centrifugation 5 min at 600g and resuspended in 600 µl of 13U/ml Liberase DH Research Grade Sigma #5401054001 in HBSS Gibso #14025 092 and incubated at 37 C for 1 h. Every 15 min 500 µl of supernatant was removed quenched with 65µl sheep serum Sigma S2263 on ice and 500 µl of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 µl filters Corning #431750 pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure Invitrogen AM2616. Before sorting 1 µg/ml DAPI Sigma D9542 was added to the tube.,fluorescence:osx:H2A mCherry+ osx:Venus hGeminin+|cell type:osteoblasts of regenerating zebrafish scales,GSM4433142,GSM4433142: high Erk activity; rep2; Danio rerio; RNA Seq,GSM4433142,,1,RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation – BT01,GEO Accession:GSM4433142,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP254053,,,5G_plus_1.fq.gz 5G_plus_2.fq.gz,fastq fastq,4708623600.0,47086236.0,GSM4433142 r1,0:100 1:100,A:1200601624;C:1150903127;G:1136628277;T:1220490572;N:0,100,100,,,1200601624,1150903127,1136628277,1220490572,0,SRX8003656,SRS6377636,SRA1059429,GEO,"Poss, Cell Biology, Duke University",1,0.90729,,0.03751,,0.84433,,0.50342,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,United States,2020-03-25,Undetermined,Undetermined,Bone or Cartilage,Skeletal Element 74701,SRR24003726,SRX19807142,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 4,case2 4,Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_4_1.fq.gz case2_4_2.fq.gz,fastq fastq,6631325400.0,22104418.0,case2 4 1.fq.gz,0:150 1:150,A:1790451511;C:1523987494;G:1517049214;T:1799837181;N:0,150,150,,,1790451511,1523987494,1517049214,1799837181,0,SRX19807142,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.94202,0.94054,0.06448,0.06393,0.71415,0.71445,0.52801,0.52947,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element 74702,SRR24003727,SRX19807141,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 3,case2 3,Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_3_1.fq.gz case2_3_2.fq.gz,fastq fastq,6706743300.0,22355811.0,case2 3 1.fq.gz,0:150 1:150,A:1845685627;C:1507725453;G:1499541624;T:1853790596;N:0,150,150,,,1845685627,1507725453,1499541624,1853790596,0,SRX19807141,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.94268,0.93594,0.08009,0.07937,0.70402,0.70441,0.4556,0.48818,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element 74703,SRR24003728,SRX19807140,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 2,case2 2,Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_2_1.fq.gz case2_2_2.fq.gz,fastq fastq,6677092200.0,22256974.0,case2 2 1.fq.gz,0:150 1:150,A:1864795230;C:1474224567;G:1465199644;T:1872872759;N:0,150,150,,,1864795230,1474224567,1465199644,1872872759,0,SRX19807140,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.93359,0.92743,0.0959,0.09583,0.69089,0.69234,0.48419,0.48121,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element 74704,SRR24003729,SRX19807139,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 1,case2 1,Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_1_1.fq.gz case2_1_2.fq.gz,fastq fastq,6644478600.0,22148262.0,case2 1 1.fq.gz,0:150 1:150,A:1863814645;C:1460246773;G:1453279946;T:1867137236;N:0,150,150,,,1863814645,1460246773,1453279946,1867137236,0,SRX19807139,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.93932,0.9379,0.09722,0.09709,0.71985,0.71873,0.49646,0.5522,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element 74705,SRR24003730,SRX19807138,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,control2 6,control2 6,Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,control2_6_1.fq.gz control2_6_2.fq.gz,fastq fastq,6817849200.0,22726164.0,control2 6 1.fq.gz,0:150 1:150,A:1916198776;C:1480570561;G:1501234091;T:1919845772;N:0,150,150,,,1916198776,1480570561,1501234091,1919845772,0,SRX19807138,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.94697,0.9369,0.06934,0.06812,0.76824,0.77114,0.49005,0.54882,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element 74706,SRR24003731,SRX19807137,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,control2 5,control2 5,Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,control2_5_1.fq.gz control2_5_2.fq.gz,fastq fastq,6730171500.0,22433905.0,control2 5 1.fq.gz,0:150 1:150,A:1881763818;C:1469481635;G:1493477302;T:1885448745;N:0,150,150,,,1881763818,1469481635,1493477302,1885448745,0,SRX19807137,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.9399,0.92905,0.0832,0.08122,0.70993,0.71228,0.54991,0.58952,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element 74707,SRR24003732,SRX19807136,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,control2 4,control2 4,Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,control2_4_1.fq.gz control2_4_2.fq.gz,fastq fastq,6660686100.0,22202287.0,control2 4 1.fq.gz,0:150 1:150,A:1846205332;C:1486328129;G:1477889862;T:1850262777;N:0,150,150,,,1846205332,1486328129,1477889862,1850262777,0,SRX19807136,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.94251,0.94001,0.08206,0.082,0.69483,0.69524,0.49193,0.49602,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element 74708,SRR24003733,SRX19807135,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,control2 3,control2 3,Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,control2_3_1.fq.gz control2_3_2.fq.gz,fastq fastq,6683569500.0,22278565.0,control2 3 1.fq.gz,0:150 1:150,A:1846755716;C:1494194697;G:1482717957;T:1859901130;N:0,150,150,,,1846755716,1494194697,1482717957,1859901130,0,SRX19807135,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.93255,0.93106,0.10717,0.10731,0.67665,0.67791,0.54876,0.52297,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element 74709,SRR24003734,SRX19807134,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 7,case2 7,Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_7_1.fq.gz case2_7_2.fq.gz,fastq fastq,6770748000.0,22569160.0,case2 7 1.fq.gz,0:150 1:150,A:1918448687;C:1455131518;G:1474277741;T:1922890054;N:0,150,150,,,1918448687,1455131518,1474277741,1922890054,0,SRX19807134,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.94025,0.92953,0.08709,0.0851,0.73864,0.73914,0.5716,0.56037,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element 74710,SRR24003735,SRX19807133,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 6,case2 6,Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_6_1.fq.gz case2_6_2.fq.gz,fastq fastq,6743372700.0,22477909.0,case2 6 1.fq.gz,0:150 1:150,A:1825699499;C:1533637372;G:1552424547;T:1831611282;N:0,150,150,,,1825699499,1533637372,1552424547,1831611282,0,SRX19807133,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.95425,0.94313,0.05313,0.05246,0.77268,0.77461,0.52616,0.5227,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element 74711,SRR24003736,SRX19807132,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,case2 5,case2 5,Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,case2_5_1.fq.gz case2_5_2.fq.gz,fastq fastq,6810815400.0,22702718.0,case2 5 1.fq.gz,0:150 1:150,A:1861549181;C:1529649127;G:1553365612;T:1866251480;N:0,150,150,,,1861549181,1529649127,1553365612,1866251480,0,SRX19807132,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.94842,0.93757,0.06448,0.06317,0.74036,0.74097,0.53479,0.52393,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element 74712,SRR24003737,SRX19807131,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,control2 2,control2 2,Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,control2_2_1.fq.gz control2_2_2.fq.gz,fastq fastq,6693643800.0,22312146.0,control2 2 1.fq.gz,0:150 1:150,A:1846873501;C:1499207913;G:1490122627;T:1857439759;N:0,150,150,,,1846873501,1499207913,1490122627,1857439759,0,SRX19807131,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.93282,0.93092,0.09007,0.0899,0.68672,0.68793,0.55221,0.55318,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element 74713,SRR24003738,SRX19807130,SRS17168877,SRP429947,PRJNA949785,Sequencing of zebrafish bone tissues,PRJNA949785,Other,Transcriptomics was used to investigate sensitive genes associated with exercise improved bone mass,,,,,eight month zebrafish bone tissues,,breed:Not applicable|age:8 month|sex:male|tissue:b1|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of b1 tissue in zebrafish,control2 1,control2 1,Qualified total RNA was purified by DNase I and mRNA was enriched by adding OligodT attached magnetic beads. Subsequently fragment buffer was added to cleave the mRNA into small fragments. Fragmented mRNA was used as a template for reverse transcription to generate the first cDNA strand and then the second cDNA strand was generated. End repair and adaptor ligation were performed by adding A tailing Mix and RNA Index Adapters and then PCR amplification was performed. Single strand circle DNA library was obtained by recovering and cycling the PCR products. The final library was obtained by purifying the linear DNA molecules that were not cycled. The quality of the final library was tested. The qualified library was replicated by rolling circle replication to form DNA nanospheres DNBs. DNBs were added to the mesh holes of a nanochip using high density DNA nanochip technology. Subsequently sequencing was performed on the BGIISEQ500 platform BGI Shenzhen Guangdong China using combined probe anchored polymerisation.,,,RNA-Seq,TRANSCRIPTOMIC,PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP429947,,,control2_1_1.fq.gz control2_1_2.fq.gz,fastq fastq,6629354100.0,22097847.0,control2 1 1.fq.gz,0:150 1:150,A:1819412655;C:1492313439;G:1486507818;T:1831120188;N:0,150,150,,,1819412655,1492313439,1486507818,1831120188,0,SRX19807130,SRS17168877,SRA1612461,"Sun Yat-sen University|Department of Epidemiology, School of Public Healt",Sun Yat-sen University,2,0.93273,0.93086,0.08814,0.08711,0.67748,0.67696,0.5355,0.54253,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2023-03-29,Adult,Adult,Bone or Cartilage,Skeletal Element