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 28794,SRR26685983,SRX22385777,SRS19431939,SRP470412,PRJNA1036238,RNAseq of Wild Type and pikfyve?8 zebrafish.,GSE247110,Transcriptome Analysis,Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.,,,,pikfyve3,GSM7883488,,source name:genotype|tissue:genotype|genotype:pikfyve delta8|geo loc name:missing|collection date:missing,pikfyve3,Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample,genotype,,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing,,tissue:genotype|genotype:pikfyve delta8,GSM7883488,GSM7883488: pikfyve3; Danio rerio; RNA Seq,GSM7883488 r1,GSM7883488,1,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP470412,,,pikfyve3_1.fq.gz pikfyve3_2.fq.gz,fastq fastq,6618846900.0,22062823.0,GSM7883488 r1,0:150 1:150,A:1763884594;C:1537497822;G:1533232898;T:1784136042;N:95544,150,150,,,1763884594,1537497822,1533232898,1784136042,95544,SRX22385777,SRS19431939,SRA1746433,"The Second Clinical Medical College, Jinan University","The Second Clinical Medical College, Jinan University",2,0.93396,0.92718,0.09419,0.09305,0.66348,0.66496,0.48704,0.4839,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-06,Undetermined,Undetermined,Undetermined,Undetermined 28795,SRR26685984,SRX22385776,SRS19431938,SRP470412,PRJNA1036238,RNAseq of Wild Type and pikfyve?8 zebrafish.,GSE247110,Transcriptome Analysis,Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.,,,,pikfyve2,GSM7883487,,source name:genotype|tissue:genotype|genotype:pikfyve delta8|geo loc name:missing|collection date:missing,pikfyve2,Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample,genotype,,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing,,tissue:genotype|genotype:pikfyve delta8,GSM7883487,GSM7883487: pikfyve2; Danio rerio; RNA Seq,GSM7883487 r1,GSM7883487,1,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP470412,,,pikfyve2_1.fq.gz pikfyve2_2.fq.gz,fastq fastq,6640406100.0,22134687.0,GSM7883487 r1,0:150 1:150,A:1765647548;C:1547424271;G:1541609810;T:1785639698;N:84773,150,150,,,1765647548,1547424271,1541609810,1785639698,84773,SRX22385776,SRS19431938,SRA1746433,"The Second Clinical Medical College, Jinan University","The Second Clinical Medical College, Jinan University",2,0.93535,0.92946,0.08654,0.08582,0.67127,0.67298,0.48517,0.48183,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-06,Undetermined,Undetermined,Undetermined,Undetermined 28796,SRR26685985,SRX22385775,SRS19431937,SRP470412,PRJNA1036238,RNAseq of Wild Type and pikfyve?8 zebrafish.,GSE247110,Transcriptome Analysis,Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.,,,,pikfyve1,GSM7883486,,source name:genotype|tissue:genotype|genotype:pikfyve delta8|geo loc name:missing|collection date:missing,pikfyve1,Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample,genotype,,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing,,tissue:genotype|genotype:pikfyve delta8,GSM7883486,GSM7883486: pikfyve1; Danio rerio; RNA Seq,GSM7883486 r1,GSM7883486,1,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP470412,,,pikfyve1_1.fq.gz pikfyve1_2.fq.gz,fastq fastq,6629613600.0,22098712.0,GSM7883486 r1,0:150 1:150,A:1765377736;C:1543131511;G:1535515864;T:1785505926;N:82563,150,150,,,1765377736,1543131511,1535515864,1785505926,82563,SRX22385775,SRS19431937,SRA1746433,"The Second Clinical Medical College, Jinan University","The Second Clinical Medical College, Jinan University",2,0.93638,0.92994,0.08782,0.08654,0.67138,0.67119,0.47859,0.47753,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-06,Undetermined,Undetermined,Undetermined,Undetermined 28797,SRR26685986,SRX22385774,SRS19431936,SRP470412,PRJNA1036238,RNAseq of Wild Type and pikfyve?8 zebrafish.,GSE247110,Transcriptome Analysis,Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.,,,,WT3,GSM7883485,,source name:genotype|tissue:genotype|genotype:Wile Type|geo loc name:missing|collection date:missing,WT3,Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample,genotype,,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing,,tissue:genotype|genotype:Wile Type,GSM7883485,GSM7883485: WT3; Danio rerio; RNA Seq,GSM7883485 r1,GSM7883485,1,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP470412,,,WT3_2.fq.gz WT3_1.fq.gz,fastq fastq,6654357000.0,22181190.0,GSM7883485 r1,0:150 1:150,A:1778694761;C:1540249434;G:1534346559;T:1801052542;N:13704,150,150,,,1778694761,1540249434,1534346559,1801052542,13704,SRX22385774,SRS19431936,SRA1746433,"The Second Clinical Medical College, Jinan University","The Second Clinical Medical College, Jinan University",2,0.93688,0.92644,0.09182,0.09071,0.66229,0.66434,0.48313,0.48263,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-06,Undetermined,Undetermined,Undetermined,Undetermined 28798,SRR26685987,SRX22385773,SRS19431935,SRP470412,PRJNA1036238,RNAseq of Wild Type and pikfyve?8 zebrafish.,GSE247110,Transcriptome Analysis,Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.,,,,WT2,GSM7883484,,source name:genotype|tissue:genotype|genotype:Wile Type|geo loc name:missing|collection date:missing,WT2,Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample,genotype,,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing,,tissue:genotype|genotype:Wile Type,GSM7883484,GSM7883484: WT2; Danio rerio; RNA Seq,GSM7883484 r1,GSM7883484,1,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP470412,,,WT2_1.fq.gz WT2_2.fq.gz,fastq fastq,6661129500.0,22203765.0,GSM7883484 r1,0:150 1:150,A:1774160269;C:1545605554;G:1545211257;T:1796139014;N:13406,150,150,,,1774160269,1545605554,1545211257,1796139014,13406,SRX22385773,SRS19431935,SRA1746433,"The Second Clinical Medical College, Jinan University","The Second Clinical Medical College, Jinan University",2,0.93696,0.9278,0.08665,0.08477,0.66322,0.66498,0.48376,0.48557,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-06,Undetermined,Undetermined,Undetermined,Undetermined 28799,SRR26685988,SRX22385772,SRS19431934,SRP470412,PRJNA1036238,RNAseq of Wild Type and pikfyve?8 zebrafish.,GSE247110,Transcriptome Analysis,Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish.,,,,WT1,GSM7883483,,source name:genotype|tissue:genotype|genotype:Wile Type|geo loc name:missing|collection date:missing,WT1,Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample,genotype,,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing,,tissue:genotype|genotype:Wile Type,GSM7883483,GSM7883483: WT1; Danio rerio; RNA Seq,GSM7883483 r1,GSM7883483,1,The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP470412,,,WT1_2.fq.gz WT1_1.fq.gz,fastq fastq,6648386700.0,22161289.0,GSM7883483 r1,0:150 1:150,A:1780975057;C:1536473791;G:1530388485;T:1800462718;N:86649,150,150,,,1780975057,1536473791,1530388485,1800462718,86649,SRX22385772,SRS19431934,SRA1746433,"The Second Clinical Medical College, Jinan University","The Second Clinical Medical College, Jinan University",2,0.93595,0.92974,0.09487,0.09314,0.65969,0.66005,0.48731,0.4845,150,150,B,B,biological fallback assumption,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,China,2023-11-06,Undetermined,Undetermined,Undetermined,Undetermined 30691,SRR28270998,SRX23880961,SRS20704477,SRP494117,PRJNA1085662,Roxithromycin exposure induces motoneuron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells,PRJNA1085662,Other,Roxithromycin ROX a commonly used macrolide antibiotic is extensively employed in human medicine and livestock industries. Due to its structural stability and resistance to biological degradation ROX persists as a resilient environmental contaminant detectable in aquatic ecosystems and food products. However our understanding of the potential health risks to humans from continuous ROX exposure remains limited. In this study we used the zebrafish as a vertebrate model to explore the potential developmental toxicity of early ROX exposure particularly focusing on its effects on locomotor functionality and motoneuron development. Early exposure to ROX induces marked developmental toxicity in zebrafish embryos significantly reducing hatch rates body lengths and increased malformation rates. Moreover ROX exposure adversely affected the locomotive capacity of zebrafish embryos and observations in transgenic zebrafish Tghb9:eGFP revealed axonal loss in motor neurons evident through reduced or irregular axonal lengths. Concurrently abnormal apoptosis in ROX exposed zebrafish embryos intensified alongside the upregulation of apoptosis related genes bax bcl2 caspase 3a. Single cell sequencing further disclosed substantial effects of ROX on genes involved in the differentiation of motor neuron progenitor cells ngn1 olig2 axon development cd82a mbpa plp1b sema5a and neuroimmunity aplnrb aplnra in zebrafish larvae. Furthermore the motor neuron defects induced by ROX can be rescued by administering ngn1 agonist. In summary ROX exposure leads to early life abnormalities in zebrafish motor neurons and locomotor behavior by hindering the differentiation of motor neuron progenitor cells and inducing abnormal apoptosis.,,,,,WT,,strain:not provided|isolate:not provided|breed:not provided|cultivar:not provided|ecotype:not provided|age:not provided|dev stage:not provided|collection date:not provided|geo loc name:not provided|sex:not provided|tissue:Cerebrum|BioSampleModel:Model organism or animal,,,,,,,,,Roxithromycin exposure induces mot1uron malformation and behavioral deficits of zebrafish by interfering with the differentiation of motor neuron progenitor cells,DANIO,DANIO,Illumina Second Generation Sequencing,,,RNA-Seq,TRANSCRIPTOMIC,cDNA_oligo_dT,SINGLE,BGISEQ,BGISEQ-500,,SRP494117,,,WT_S1_L001_I1_001.fastq.gz,fastq,7991376264.0,998922033.0,WT S1 L001 I1 001.fastq.gz,0:8,A:2573734851;C:1426474966;G:1492966198;T:2498173074;N:27175,8,,,,2573734851,1426474966,1492966198,2498173074,27175,SRX23880961,SRS20704477,SRA1820072,shantou university|Neurobiology Center,shantou university,1,0.0,,0.0,,1.0,,,,8,,T,,under 1.2% mapping rate,bgi,bgi,unknown,poly_a,unknown,sc_generic,single_cell_generic,generic-scrnaseq-only,,China,2024-03-11,Undetermined,Multi-stage,Brain,Nervous System 48009,SRR6910782,SRX3858788,SRS3106147,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart yap sham 3,GSM3070341,,tissue:7 xxx post injury sham yap mutant zebrafish heart replicate 3|injury type:Sham Injured|genotype:yap / ,zebrafish heart yap sham 3,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury sham yap mutant zebrafish heart replicate 3,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Sham Injured|genotype:yap / ,GSM3070341,GSM3070341: zebrafish heart yap sham 3; Danio rerio; RNA Seq,GSM3070341,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070341,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAFRACPEI-39_1.fq.gz,fastq,951999850.0,19039997.0,GSM3070341 r1,0:50,A:264195948;C:210535284;G:216206679;T:260149711;N:912228,50,,,,264195948,210535284,216206679,260149711,912228,SRX3858788,SRS3106147,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.94079,,0.07209,,0.77506,,0.57202,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System 48010,SRR6910781,SRX3858787,SRS3106141,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart yap sham 2,GSM3070340,,tissue:7 xxx post injury sham yap mutant zebrafish heart replicate 2|injury type:Sham Injured|genotype:yap / ,zebrafish heart yap sham 2,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury sham yap mutant zebrafish heart replicate 2,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Sham Injured|genotype:yap / ,GSM3070340,GSM3070340: zebrafish heart yap sham 2; Danio rerio; RNA Seq,GSM3070340,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070340,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAERABPEI-38_1.fq.gz,fastq,1422243650.0,28444873.0,GSM3070340 r1,0:50,A:396912878;C:311739320;G:316711298;T:395335784;N:1544370,50,,,,396912878,311739320,316711298,395335784,1544370,SRX3858787,SRS3106141,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.92453,,0.08919,,0.75402,,0.56482,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System 48011,SRR6910780,SRX3858786,SRS3106146,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart yap sham 1,GSM3070339,,tissue:7 xxx post injury sham yap mutant zebrafish heart replicate 1|injury type:Sham Injured|genotype:yap / ,zebrafish heart yap sham 1,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury sham yap mutant zebrafish heart replicate 1,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Sham Injured|genotype:yap / ,GSM3070339,GSM3070339: zebrafish heart yap sham 1; Danio rerio; RNA Seq,GSM3070339,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070339,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAADRABPEI-35_1.fq.gz,fastq,1414732800.0,28294656.0,GSM3070339 r1,0:50,A:382546700;C:323161121;G:333740729;T:373569891;N:1714359,50,,,,382546700,323161121,333740729,373569891,1714359,SRX3858786,SRS3106146,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93663,,0.06374,,0.78476,,0.50181,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System 48012,SRR6910779,SRX3858785,SRS3106140,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart yap cryo 3,GSM3070338,,tissue:7 xxx post injury cryoinjury yap mutant zebrafish heart replicate 3|injury type:Cryoinjured|genotype:yap / ,zebrafish heart yap cryo 3,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury cryoinjury yap mutant zebrafish heart replicate 3,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Cryoinjured|genotype:yap / ,GSM3070338,GSM3070338: zebrafish heart yap cryo 3; Danio rerio; RNA Seq,GSM3070338,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070338,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAALRABPEI-45_1.fq.gz,fastq,1417604550.0,28352091.0,GSM3070338 r1,0:50,A:396320928;C:310857539;G:315507312;T:393521845;N:1396926,50,,,,396320928,310857539,315507312,393521845,1396926,SRX3858785,SRS3106140,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93466,,0.08509,,0.76339,,0.55298,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System 48013,SRR6910778,SRX3858784,SRS3106139,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart yap cryo 2,GSM3070337,,tissue:7 xxx post injury cryoinjury yap mutant zebrafish heart replicate 2|injury type:Cryoinjured|genotype:yap / ,zebrafish heart yap cryo 2,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury cryoinjury yap mutant zebrafish heart replicate 2,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Cryoinjured|genotype:yap / ,GSM3070337,GSM3070337: zebrafish heart yap cryo 2; Danio rerio; RNA Seq,GSM3070337,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070337,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAKRABPEI-44_1.fq.gz,fastq,1411684000.0,28233680.0,GSM3070337 r1,0:50,A:380723872;C:320871596;G:326847305;T:381926882;N:1314345,50,,,,380723872,320871596,326847305,381926882,1314345,SRX3858784,SRS3106139,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93583,,0.07153,,0.76209,,0.53446,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System 48014,SRR6910777,SRX3858783,SRS3106138,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart yap cryo 1,GSM3070336,,tissue:7 xxx post injury cryoinjury yap mutant zebrafish heart replicate 1|injury type:Cryoinjured|genotype:yap / ,zebrafish heart yap cryo 1,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury cryoinjury yap mutant zebrafish heart replicate 1,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Cryoinjured|genotype:yap / ,GSM3070336,GSM3070336: zebrafish heart yap cryo 1; Danio rerio; RNA Seq,GSM3070336,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070336,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170901_I13_CL100030164_L2_HK500ZEBljgRAAARAAPEI-2_1.fq.gz,fastq,983464900.0,19669298.0,GSM3070336 r1,0:50,A:281927620;C:213905948;G:225993312;T:260949314;N:688706,50,,,,281927620,213905948,225993312,260949314,688706,SRX3858783,SRS3106138,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93596,,0.08164,,0.75753,,0.5319,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System 48015,SRR6910776,SRX3858782,SRS3106137,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart wt sham 3,GSM3070335,,tissue:7 xxx post injury sham wildtype zebrafish heart replicate 3|injury type:Sham Injured|genotype:yap +/+,zebrafish heart wt sham 3,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury sham wildtype zebrafish heart replicate 3,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Sham Injured|genotype:yap +/+,GSM3070335,GSM3070335: zebrafish heart wt sham 3; Danio rerio; RNA Seq,GSM3070335,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070335,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAACRABPEI-34_1.fq.gz,fastq,1422074600.0,28441492.0,GSM3070335 r1,0:50,A:391714900;C:316763778;G:323715902;T:388371260;N:1508760,50,,,,391714900,316763778,323715902,388371260,1508760,SRX3858782,SRS3106137,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93511,,0.06875,,0.78374,,0.5442,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System 48016,SRR6910775,SRX3858781,SRS3106142,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart wt sham 2,GSM3070334,,tissue:7 xxx post injury sham wildtype zebrafish heart replicate 2|injury type:Sham Injured|genotype:yap +/+,zebrafish heart wt sham 2,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury sham wildtype zebrafish heart replicate 2,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Sham Injured|genotype:yap +/+,GSM3070334,GSM3070334: zebrafish heart wt sham 2; Danio rerio; RNA Seq,GSM3070334,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070334,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAABRABPEI-32_1.fq.gz,fastq,1422698650.0,28453973.0,GSM3070334 r1,0:50,A:393538224;C:315070062;G:319739652;T:393085965;N:1264747,50,,,,393538224,315070062,319739652,393085965,1264747,SRX3858781,SRS3106142,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93436,,0.08499,,0.76599,,0.51331,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System 48017,SRR6910774,SRX3858780,SRS3106135,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart wt sham 1,GSM3070333,,tissue:7 xxx post injury sham wildtype zebrafish heart replicate 1|injury type:Sham Injured|genotype:yap +/+,zebrafish heart wt sham 1,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury sham wildtype zebrafish heart replicate 1,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Sham Injured|genotype:yap +/+,GSM3070333,GSM3070333: zebrafish heart wt sham 1; Danio rerio; RNA Seq,GSM3070333,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070333,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAARAAPEI-30_1.fq.gz,fastq,1421323500.0,28426470.0,GSM3070333 r1,0:50,A:398883510;C:309497967;G:316648847;T:394532024;N:1761152,50,,,,398883510,309497967,316648847,394532024,1761152,SRX3858780,SRS3106135,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93565,,0.0827,,0.77749,,0.54321,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System 48018,SRR6910773,SRX3858779,SRS3106136,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart wt cryo 3,GSM3070332,,tissue:7 xxx post injury cryoinjury wildtype zebrafish heart replicate 3|injury type:Cryoinjured|genotype:yap +/+,zebrafish heart wt cryo 3,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury cryoinjury wildtype zebrafish heart replicate 3,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Cryoinjured|genotype:yap +/+,GSM3070332,GSM3070332: zebrafish heart wt cryo 3; Danio rerio; RNA Seq,GSM3070332,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070332,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAIRABPEI-42_1.fq.gz,fastq,1420446700.0,28408934.0,GSM3070332 r1,0:50,A:390252025;C:317481829;G:322013373;T:389237056;N:1462417,50,,,,390252025,317481829,322013373,389237056,1462417,SRX3858779,SRS3106136,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.92817,,0.08055,,0.75304,,0.54626,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System 48019,SRR6910772,SRX3858778,SRS3106133,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart wt cryo 2,GSM3070331,,tissue:7 xxx post injury cryoinjury wildtype zebrafish heart replicate 2|injury type:Cryoinjured|genotype:yap +/+,zebrafish heart wt cryo 2,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury cryoinjury wildtype zebrafish heart replicate 2,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Cryoinjured|genotype:yap +/+,GSM3070331,GSM3070331: zebrafish heart wt cryo 2; Danio rerio; RNA Seq,GSM3070331,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070331,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAHRABPEI-41_1.fq.gz,fastq,1422338300.0,28446766.0,GSM3070331 r1,0:50,A:393674065;C:315125662;G:322045666;T:389932855;N:1560052,50,,,,393674065,315125662,322045666,389932855,1560052,SRX3858778,SRS3106133,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.9294,,0.08412,,0.75749,,0.52514,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System 48020,SRR6910771,SRX3858777,SRS3106134,SRP136723,PRJNA447594,RNAseq of regenerating yap mutant zebrafish hearts,GSE112452,Transcriptome Analysis,A Yap knockout zebrafish line was used to observe how loss of Yap affects cardiac regeneration. Overall design: Cryoinjury or sham surgeries were performed on 6 mpf 12 mpf zebrafish ventricles. At 7 xxx post injury whole hearts were collected and RNAseq was performed.,,pubmed:30295714,,zebrafish heart wt cryo 1,GSM3070330,,tissue:7 xxx post injury cryoinjury wildtype zebrafish heart replicate 1|injury type:Cryoinjured|genotype:yap +/+,zebrafish heart wt cryo 1,"Primary sequencing data was conducted with a BGISEQ 500 50SE at 20M reads per sample. Raw reads are subjected to quality control QC to determine if a resequencing step is needed. post QC raw reads are filtered into clean reads which are aligned to the reference sequences. ""Dirty"" raw reads are reads which contain the sequence of adaptor high content of unknown bases and low quality reads and are removed before analysis. Bowtie2 was used to map clean reads to reference gene and HISAT used to reference genome. The Fragments Per Kilobase of transcript per Million mapped reads FPKM method is used to calculated expression level. Genome build: GRCz11 Supplementary files format and content: Excel files containing FKPM values for expression levels.",7 xxx post injury cryoinjury wildtype zebrafish heart replicate 1,Zebrafish were anesthetized in 0.02% tricaine. An incision was made through the chest to gain access to the heart. Ventricles were exposed for roughly four seconds to a 0.5mm liquid nitrogen chilled stainless steel probe for cryoinjury or left alone for sham injury,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,Zebrafish Danio rerio were maintained at 28.5C on an Aquatic Habitats recirculating filtered water system in reverse osmosis purified water supplemented with Instant Ocean salts 60 mg/l on a 14 h light:10 h dark lighting cycle and fed a standard diet.,injury type:Cryoinjured|genotype:yap +/+,GSM3070330,GSM3070330: zebrafish heart wt cryo 1; Danio rerio; RNA Seq,GSM3070330,,1,RNA was extracted using Trizol Thermo Fisher Scientific phenol cholorform extraction. RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low input poly A BGISEQ 500RSRNASeqTranscriptome protocol.,GEO Accession:GSM3070330,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP136723,,,170715_I13_CL100028033_L1_HK500ZEBvisRAAGRABPEI-40_1.fq.gz,fastq,1419380450.0,28387609.0,GSM3070330 r1,0:50,A:393618390;C:313492075;G:321642338;T:389289283;N:1338364,50,,,,393618390,313492075,321642338,389289283,1338364,SRX3858777,SRS3106134,SRA675997,GEO,"Brian Link, Cell Biology, Neurobiology, & Anatomy, Medical College of Wisconsin",1,0.93599,,0.08586,,0.75381,,0.52578,,50,,B,,usable mapping rate,bgi,bgi,unknown,poly_a,unknown,bulk,unknown,unknown,,United States,2018-03-28,Undetermined,Adult,Heart,Cardiovascular System 55373,SRR10322141,SRX7032952,SRS5553012,SRP226571,PRJNA578840,RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4,GSE139226,Transcriptome Analysis,RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter. Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. Normal thymus cells were also harvested from control zebrafish lck mCherry.,,pubmed:35504924,,IRF4 overexpression with p53 mutation RNA seq #2,GSM4134351,,tissue:lck IRF4;p53+/ |genotype/variation:IRF4 overexpression and p53 mutation,IRF4 overexpression with p53 mutation RNA seq #2,RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/ were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4 with the intersection strict mode was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts differentially expressed genes,lck IRF4;p53+/ ,No treatment,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,genotype/variation:IRF4 overexpression and p53 mutation,GSM4134351,GSM4134351: IRF4 overexpression with p53 mutation RNA seq #2; Danio rerio; RNA Seq,GSM4134351,,1,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM4134351,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP226571,,,IRF4xp53_3_1.fastq.gz IRF4xp53_3_2.fastq.gz,fastq fastq,8647695276.0,86535602.0,GSM4134351 r1,0:99.93 1:99.93,A:2336303355;C:1960332457;G:1974896588;T:2376162876;N:0,99,99,,,2336303355,1960332457,1974896588,2376162876,0,SRX7032952,SRS5553012,SRA982884,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94146,,0.26739,,0.77739,,0.49821,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2019-10-22,Undetermined,Undetermined,Multi-tissue,Multi-system 55374,SRR10322140,SRX7032951,SRS5553011,SRP226571,PRJNA578840,RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4,GSE139226,Transcriptome Analysis,RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter. Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. Normal thymus cells were also harvested from control zebrafish lck mCherry.,,pubmed:35504924,,IRF4 overexpression with p53 mutation RNA seq #1,GSM4134350,,tissue:lck IRF4;p53+/ |genotype/variation:IRF4 overexpression and p53 mutation,IRF4 overexpression with p53 mutation RNA seq #1,RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/ were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4 with the intersection strict mode was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts differentially expressed genes,lck IRF4;p53+/ ,No treatment,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,genotype/variation:IRF4 overexpression and p53 mutation,GSM4134350,GSM4134350: IRF4 overexpression with p53 mutation RNA seq #1; Danio rerio; RNA Seq,GSM4134350,,1,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM4134350,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP226571,,,IRF4xp53_1_1.fastq.gz IRF4xp53_1_2.fastq.gz,fastq fastq,8579468052.0,85855086.0,GSM4134350 r1,0:99.93 1:99.93,A:2293476693;C:1963039176;G:1985578185;T:2337373998;N:0,99,99,,,2293476693,1963039176,1985578185,2337373998,0,SRX7032951,SRS5553011,SRA982884,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94576,,0.27683,,0.77589,,0.47851,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2019-10-22,Undetermined,Undetermined,Multi-tissue,Multi-system 55375,SRR10322139,SRX7032950,SRS5553010,SRP226571,PRJNA578840,RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4,GSE139226,Transcriptome Analysis,RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter. Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. Normal thymus cells were also harvested from control zebrafish lck mCherry.,,pubmed:35504924,,IRF4 overexpression RNA seq #2,GSM4134349,,tissue:lck IRF4|genotype/variation:IRF4 overexpression,IRF4 overexpression RNA seq #2,RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/ were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4 with the intersection strict mode was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts differentially expressed genes,lck IRF4,No treatment,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,genotype/variation:IRF4 overexpression,GSM4134349,GSM4134349: IRF4 overexpression RNA seq #2; Danio rerio; RNA Seq,GSM4134349,,1,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM4134349,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP226571,,,IRF4_2_1.fastq.gz IRF4_2_2.fastq.gz,fastq fastq,8625409426.0,86311782.0,GSM4134349 r1,0:99.93 1:99.93,A:2345513123;C:1941948054;G:1962855201;T:2375093048;N:0,99,99,,,2345513123,1941948054,1962855201,2375093048,0,SRX7032950,SRS5553010,SRA982884,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94815,,0.35561,,0.79117,,0.50866,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2019-10-22,Undetermined,Undetermined,Multi-tissue,Multi-system 55376,SRR10322138,SRX7032949,SRS5553009,SRP226571,PRJNA578840,RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4,GSE139226,Transcriptome Analysis,RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter. Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. Normal thymus cells were also harvested from control zebrafish lck mCherry.,,pubmed:35504924,,IRF4 overexpression RNA seq #1,GSM4134348,,tissue:lck IRF4|genotype/variation:IRF4 overexpression,IRF4 overexpression RNA seq #1,RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/ were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4 with the intersection strict mode was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts differentially expressed genes,lck IRF4,No treatment,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,genotype/variation:IRF4 overexpression,GSM4134348,GSM4134348: IRF4 overexpression RNA seq #1; Danio rerio; RNA Seq,GSM4134348,,1,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM4134348,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP226571,,,IRF4_1_1.fastq.gz IRF4_1_2.fastq.gz,fastq fastq,8560288616.0,85661544.0,GSM4134348 r1,0:99.93 1:99.93,A:2300488079;C:1940898245;G:1978951452;T:2339950840;N:0,99,99,,,2300488079,1940898245,1978951452,2339950840,0,SRX7032949,SRS5553009,SRA982884,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94019,,0.24387,,0.75789,,0.49007,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2019-10-22,Undetermined,Undetermined,Multi-tissue,Multi-system 55377,SRR10322137,SRX7032948,SRS5553008,SRP226571,PRJNA578840,RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4,GSE139226,Transcriptome Analysis,RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter. Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. Normal thymus cells were also harvested from control zebrafish lck mCherry.,,pubmed:35504924,,mCherry control RNA seq #2,GSM4134347,,tissue:lck mCherry|genotype/variation:control,mCherry control RNA seq #2,RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/ were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4 with the intersection strict mode was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts differentially expressed genes,lck mCherry,No treatment,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,genotype/variation:control,GSM4134347,GSM4134347: mCherry control RNA seq #2; Danio rerio; RNA Seq,GSM4134347,,1,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM4134347,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP226571,,,Lck_mch_2_1.fastq.gz Lck_mch_2_2.fastq.gz,fastq fastq,8556568306.0,85629202.0,GSM4134347 r1,0:99.93 1:99.93,A:2299427498;C:1945648999;G:1981590842;T:2329900967;N:0,99,99,,,2299427498,1945648999,1981590842,2329900967,0,SRX7032948,SRS5553008,SRA982884,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94792,,0.25274,,0.80085,,0.51772,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2019-10-22,Undetermined,Undetermined,Multi-tissue,Multi-system 55378,SRR10322136,SRX7032947,SRS5553007,SRP226571,PRJNA578840,RNA seq analysis for zebrafish tumors driven by overexpression of human IRF4,GSE139226,Transcriptome Analysis,RNA seq analysis was performed using zebrafish primary tumors and control thymus to analyze gene expression changes post IRF4 overexpression. Overall design: Human IRF4 gene was overexpressed under the zebrafish lck promoter. Tumor cells were harvested from IRF4 transgenic zebrafish lck IRF4 with or without xxx p53 mutation. Normal thymus cells were also harvested from control zebrafish lck mCherry.,,pubmed:35504924,,mCherry control RNA seq #1,GSM4134346,,tissue:lck mCherry|genotype/variation:control,mCherry control RNA seq #1,RNA seq datasets of two control thymus samples and four tumor samples two from lck:IRF4 and two from lRF4;p53+/ were aligned to the zebrafish genome GRCz11 using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount v1.6.1 was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation GRCz11 gtf file Bioconductor package DESeq2 v1.12.4 with the intersection strict mode was used to analyze differential gene expression. Genome build: GRCz11 Supplementary files format and content: txt files for raw counts differentially expressed genes,lck mCherry,No treatment,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Normal thymus were also harvested from control zebrafish which was transduced only with mCherry. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,genotype/variation:control,GSM4134346,GSM4134346: mCherry control RNA seq #1; Danio rerio; RNA Seq,GSM4134346,,1,Total RNA was harvested using the Qiagen miRNeasy kit. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM4134346,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP226571,,,Lck_mch_1_1.fastq.gz Lck_mch_1_2.fastq.gz,fastq fastq,8544218824.0,85502654.0,GSM4134346 r1,0:99.93 1:99.93,A:2294044731;C:1942271608;G:1967598065;T:2340304420;N:0,99,99,,,2294044731,1942271608,1967598065,2340304420,0,SRX7032947,SRS5553007,SRA982884,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94337,,0.28212,,0.79239,,0.47106,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2019-10-22,Undetermined,Undetermined,Multi-tissue,Multi-system 58533,SRR11355387,SRX7957249,SRS6343356,SRP253408,PRJNA613558,Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture,PRJNA613558,Other,As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.,,,,C2 3,C2 3,,strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2 320200327,C2 320200327,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP253408,,,C2_3_1.fq.gz C2_3_2.fq.gz,fastq fastq,6857650800.0,45717672.0,C2 3 1.fq.gz,0:150 1:150,A:1826466263;C:1599272942;G:1580689630;T:1851144875;N:77090,150,150,,,1826466263,1599272942,1580689630,1851144875,77090,SRX7957249,SRS6343356,SRA1056819,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93222,,0.02854,,0.75138,,0.50759,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-20,Undetermined,Adult,Gonad,Reproductive System 58534,SRR11355388,SRX7957248,SRS6343355,SRP253408,PRJNA613558,Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture,PRJNA613558,Other,As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.,,,,C2 2,C2 2,,strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2 220200326,C2 220200326,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP253408,,,C2_2_1.fq.gz C2_2_2.fq.gz,fastq fastq,6859954800.0,45733032.0,C2 2 1.fq.gz,0:150 1:150,A:1836618967;C:1591135182;G:1572318102;T:1859806048;N:76501,150,150,,,1836618967,1591135182,1572318102,1859806048,76501,SRX7957248,SRS6343355,SRA1056819,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93237,,0.03248,,0.74663,,0.5081,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-20,Undetermined,Adult,Gonad,Reproductive System 58535,SRR11355389,SRX7957247,SRS6343354,SRP253408,PRJNA613558,Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture,PRJNA613558,Other,As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.,,,,C2 1,C2 1,,strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2 120200325,C2 120200325,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP253408,,,C2_1_1.fq.gz C2_1_2.fq.gz,fastq fastq,6618974400.0,44126496.0,C2 1 1.fq.gz,0:150 1:150,A:1774116288;C:1533828286;G:1511526952;T:1799423408;N:79466,150,150,,,1774116288,1533828286,1511526952,1799423408,79466,SRX7957247,SRS6343354,SRA1056819,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.9326,,0.02973,,0.75426,,0.50678,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-20,Undetermined,Adult,Gonad,Reproductive System 58536,SRR11355390,SRX7957246,SRS6343353,SRP253408,PRJNA613558,Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture,PRJNA613558,Other,As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.,,,,C1 3,C1 3,,strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1 320200324,C1 320200324,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP253408,,,C1_3_1.fq.gz C1_3_2.fq.gz,fastq fastq,6837729600.0,45584864.0,C1 3 1.fq.gz,0:150 1:150,A:1831266308;C:1587032733;G:1565071069;T:1853950421;N:409069,150,150,,,1831266308,1587032733,1565071069,1853950421,409069,SRX7957246,SRS6343353,SRA1056819,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93541,,0.03212,,0.74681,,0.50268,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-20,Undetermined,Adult,Gonad,Reproductive System 58537,SRR11355391,SRX7957245,SRS6343352,SRP253408,PRJNA613558,Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture,PRJNA613558,Other,As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.,,,,C1 2,C1 2,,strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1 220200323,C1 220200323,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP253408,,,C1_2_2.fq.gz C1_2_1.fq.gz,fastq fastq,6860328000.0,45735520.0,C1 2 1.fq.gz,0:150 1:150,A:1838176072;C:1591277709;G:1569605888;T:1861063734;N:204597,150,150,,,1838176072,1591277709,1569605888,1861063734,204597,SRX7957245,SRS6343352,SRA1056819,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93763,,0.033,,0.74617,,0.50287,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-20,Undetermined,Adult,Gonad,Reproductive System 58538,SRR11355392,SRX7957244,SRS6343351,SRP253408,PRJNA613558,Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture,PRJNA613558,Other,As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.,,,,C1 1,C1 1,,strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1 120200322,C1 120200322,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP253408,,,C1_1_1.fq.gz C1_1_2.fq.gz,fastq fastq,6865547700.0,45770318.0,C1 1 1.fq.gz,0:150 1:150,A:1841774713;C:1591288582;G:1570400871;T:1861867728;N:215806,150,150,,,1841774713,1591288582,1570400871,1861867728,215806,SRX7957244,SRS6343351,SRA1056819,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93567,,0.03152,,0.74653,,0.50239,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-20,Undetermined,Adult,Gonad,Reproductive System 58539,SRR11355393,SRX7957243,SRS6343350,SRP253408,PRJNA613558,Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture,PRJNA613558,Other,As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.,,,,C0 3,C0 3,,strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 3|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0 320200321,C0 320200321,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP253408,,,C0_3_1.fq.gz C0_3_2.fq.gz,fastq fastq,6824622600.0,45497484.0,C0 3 1.fq.gz,0:150 1:150,A:1833660953;C:1578510104;G:1558095174;T:1854128169;N:228200,150,150,,,1833660953,1578510104,1558095174,1854128169,228200,SRX7957243,SRS6343350,SRA1056819,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93758,,0.0323,,0.75024,,0.50852,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-20,Undetermined,Adult,Gonad,Reproductive System 58540,SRR11355394,SRX7957242,SRS6343349,SRP253408,PRJNA613558,Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture,PRJNA613558,Other,As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.,,,,C0 2,C0 2,,strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 2|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0 220200320,C0 220200320,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP253408,,,C0_2_2.fq.gz C0_2_1.fq.gz,fastq fastq,6819326400.0,45462176.0,C0 2 1.fq.gz,0:150 1:150,A:1837661215;C:1571877614;G:1550458835;T:1859103408;N:225328,150,150,,,1837661215,1571877614,1550458835,1859103408,225328,SRX7957242,SRS6343349,SRA1056819,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93697,,0.0339,,0.74793,,0.5035,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-20,Undetermined,Adult,Gonad,Reproductive System 58541,SRR11355395,SRX7957241,SRS6343348,SRP253408,PRJNA613558,Transcriptomic assessments RNA sequencing in ovaries following treatments of gravid female zebrafish to an antibiotic mixture,PRJNA613558,Other,As the use of antimicrobials during pregnancy and the perinatal period may lead to adverse outcomes such as miscarriages and newborn disease the purpose of present study was to evaluate the influence of antibiotic exposure in offspring following treatments of gravid female zebrafish to an antibiotic mixture. For the F0 generation adult zebrafish AB strain at sexual maturity 150 dpf dpf were selected for experimentation 50% male and 50% pregnant female. Given a significant change occurred in eggs production and F1 survival at birth in present study combined with antibiotics bioaccumulated in ovary we suspect that antibiotic exposure might impact the ovary of F0 generation zebrafish and thus affect egg production and survival. Therefore ovaries of the F0 generation were evaluated for transcriptional effects in different antibiotics mixture exposure 0 1 and 100 ug/L using a HTS approach coupled with advanced bioinformatic tools.,,,,C0 1,C0 1,,strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:female|tissue:ovary|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|replicate:biological replicate 1|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0 120200319,C0 120200319,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP253408,,,C0_1_1.fq.gz C0_1_2.fq.gz,fastq fastq,7030804800.0,46872032.0,C0 1 1.fq.gz,0:150 1:150,A:1891469955;C:1624531422;G:1603124564;T:1911444454;N:234405,150,150,,,1891469955,1624531422,1603124564,1911444454,234405,SRX7957241,SRS6343348,SRA1056819,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93519,,0.0328,,0.74602,,0.48272,,150,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-03-20,Undetermined,Adult,Gonad,Reproductive System 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 60445,SRR12272862,SRX8777892,SRS7048444,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 2 4,,replicate:biological replicate 2|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200712,C2C220200712,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C2_C2_2_4.fq,fastq,542610936.0,21965958.0,C2 C2 2 4.fq.gz,0:24.70,A:95221617;C:122628624;G:167025611;T:157730855;N:4229,24,,,,95221617,122628624,167025611,157730855,4229,SRX8777892,SRS7048444,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.8119,,0.10745,,0.85717,,0.51338,,22,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures 60446,SRR12272863,SRX8777891,SRS7048443,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 1 4,,replicate:biological replicate 1|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200711,C2C220200711,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C2_C2_1_4.fq,fastq,542847476.0,22614181.0,C2 C2 1 4.fq.gz,0:24.00,A:99999101;C:125407906;G:162383758;T:155055099;N:1612,24,,,,99999101,125407906,162383758,155055099,1612,SRX8777891,SRS7048443,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.84327,,0.10491,,0.83256,,0.52046,,19,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures 60447,SRR12272864,SRX8777890,SRS7048442,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 2 4,,replicate:biological replicate 2|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200712,C1C120200712,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C1_C1_2_4.fq,fastq,570918284.0,22577002.0,C1 C1 2 4.fq.gz,0:25.29,A:100121235;C:130480588;G:178656113;T:161652765;N:7583,25,,,,100121235,130480588,178656113,161652765,7583,SRX8777890,SRS7048442,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.85096,,0.12542,,0.82873,,0.51535,,22,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures 60448,SRR12272865,SRX8777889,SRS7048441,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 1 4,,replicate:biological replicate 1|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200711,C1C120200711,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C1_C1_1_4.fq,fastq,545089417.0,22812164.0,C1 C1 1 4.fq.gz,0:23.89,A:99851844;C:125314095;G:166401335;T:153521167;N:976,23,,,,99851844,125314095,166401335,153521167,976,SRX8777889,SRS7048441,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.84602,,0.11725,,0.83159,,0.51353,,19,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures 60449,SRR12272866,SRX8777888,SRS7048440,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 2 4,,replicate:biological replicate 2|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200712,C0C020200712,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C0_C0_2_4.fq,fastq,527443144.0,23174740.0,C0 C0 2 4.fq.gz,0:22.76,A:102368401;C:120843229;G:151690193;T:152540806;N:515,22,,,,102368401,120843229,151690193,152540806,515,SRX8777888,SRS7048440,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.83063,,0.08114,,0.85169,,0.50894,,16,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures 60450,SRR12272867,SRX8777887,SRS7048439,SRP272672,PRJNA647444,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemiRNA,PRJNA647444,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 1 4,,replicate:biological replicate 1|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200711,C0C020200711,RNA seq of zebrafish in different conditions,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,BGISEQ,BGISEQ-500,,SRP272672,,loader:fastq load.py,C0_C0_1_4.fq,fastq,511759408.0,22673361.0,C0 C0 1 4.fq.gz,0:22.57,A:100879182;C:120237907;G:142799495;T:147842595;N:229,22,,,,100879182,120237907,142799495,147842595,229,SRX8777887,SRS7048439,SRA1101037,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.83904,,0.0823,,0.84741,,0.49929,,22,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-08-05,Undetermined,Embryo,Whole Organism,All anatomical structures 60496,SRR12328853,SRX8829078,SRS7048444,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 2 4,,replicate:biological replicate 2|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200712,C2C220200712,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C2_C2_2_4_1.fq.gz C2_C2_2_4_2.fq.gz,fastq fastq,6974294600.0,69742946.0,C2 C2 2 4 1.fq.gz,0:100 1:100,A:2057162032;C:1418016219;G:1425580374;T:2073535975;N:0,100,100,,,2057162032,1418016219,1425580374,2073535975,0,SRX8829078,SRS7048444,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93171,,0.17455,,0.71626,,0.54961,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures 60497,SRR12328854,SRX8829077,SRS7048443,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C2,C2 C2 1 4,,replicate:biological replicate 1|strain:AB|isolate:C2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:100ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C2C220200711,C2C220200711,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C2_C2_1_4_2.fq.gz C2_C2_1_4_1.fq.gz,fastq fastq,6942905200.0,69429052.0,C2 C2 1 4 1.fq.gz,0:100 1:100,A:2025129308;C:1433430820;G:1434784226;T:2049560846;N:0,100,100,,,2025129308,1433430820,1434784226,2049560846,0,SRX8829077,SRS7048443,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93211,,0.16662,,0.71001,,0.53674,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures 60498,SRR12328855,SRX8829076,SRS7048442,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 2 4,,replicate:biological replicate 2|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200712,C1C120200712,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C1_C1_2_4_1.fq.gz C1_C1_2_4_2.fq.gz,fastq fastq,6973657600.0,69736576.0,C1 C1 2 4 1.fq.gz,0:100 1:100,A:2050440259;C:1423350359;G:1423015668;T:2076851314;N:0,100,100,,,2050440259,1423350359,1423015668,2076851314,0,SRX8829076,SRS7048442,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.92911,,0.1877,,0.72025,,0.58085,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures 60499,SRR12328856,SRX8829075,SRS7048441,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C1,C1 C1 1 4,,replicate:biological replicate 1|strain:AB|isolate:C1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:1ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C1C120200711,C1C120200711,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C1_C1_1_4_1.fq.gz C1_C1_1_4_2.fq.gz,fastq fastq,6746729200.0,67467292.0,C1 C1 1 4 1.fq.gz,0:100 1:100,A:2004203843;C:1356765594;G:1357760526;T:2027999237;N:0,100,100,,,2004203843,1356765594,1357760526,2027999237,0,SRX8829075,SRS7048441,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.92733,,0.19903,,0.72228,,0.59259,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures 60500,SRR12328857,SRX8829074,SRS7048440,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 2 4,,replicate:biological replicate 2|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200712,C0C020200712,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C0_C0_2_4_1.fq.gz C0_C0_2_4_2.fq.gz,fastq fastq,6924724800.0,69247248.0,C0 C0 2 4 1.fq.gz,0:100 1:100,A:1974618038;C:1471821932;G:1482725702;T:1995559128;N:0,100,100,,,1974618038,1471821932,1482725702,1995559128,0,SRX8829074,SRS7048440,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93473,,0.14676,,0.69649,,0.50413,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures 60501,SRR12328858,SRX8829073,SRS7048439,SRP273655,PRJNA648800,mRNA and miRNA Seq in offspring post parental exposure to an antibiotic mixturemRNA,PRJNA648800,Other,Zebrafish embryos were exposed to environmentally relevant levels 1 and 100 ug/L of antibiotic mixtures 15 of the most commonly detected antibiotics for 150 days until sexual maturation. miRNA mRNA network analysis in offspring post parental exposure to an antibiotic mixture.,,,,C0,C0 C0 1 4,,replicate:biological replicate 1|strain:AB|isolate:C0|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:not applicable|sex:pooled male and female|tissue:the whole|collection date:2019 11 01|geo loc name:China: Shenzhen Guangdong|phenotype:0ug/L|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of zebrafish,C0C020200711,C0C020200711,RNA seq of zebrafish in different conditions,,,RNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,PAIRED,BGISEQ,BGISEQ-500,,SRP273655,,,C0_C0_1_4_1.fq.gz C0_C0_1_4_2.fq.gz,fastq fastq,6899505600.0,68995056.0,C0 C0 1 4 1.fq.gz,0:100 1:100,A:1957459931;C:1477351919;G:1482435319;T:1982258431;N:0,100,100,,,1957459931,1477351919,1482435319,1982258431,0,SRX8829073,SRS7048439,SRA1103962,Southern University of Science and Technology|School of Environmental Science and Engineering,Southern University of Science and Technology,1,0.93567,,0.14057,,0.6883,,0.48707,,100,,B,,usable mapping rate,bgi,bgi,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2020-07-27,Undetermined,Embryo,Whole Organism,All anatomical structures 65128,SRR14935651,SRX11248280,SRS9294818,SRP325966,PRJNA742218,Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing,GSE179104,Transcriptome Analysis,The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys,,pubmed:35100334,,kidney pdx1 heterozygous ko rep9,GSM5406802,,source name:total kidney|genotype:PDX1mut|tissue:kidney,kidney pdx1 heterozygous ko rep9,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,total kidney,,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,genotype:PDX1mut|tissue:kidney,GSM5406802,GSM5406802: kidney pdx1 heterozygous ko rep9; Danio rerio; RNA Seq,GSM5406802,,1,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM5406802,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP325966,,loader:fastq load.py,8724R1_18_R1_001.fastq.gz 8724R1_18_R2_001.fastq.gz,fastq fastq,11176979232.0,37097872.0,GSM5406802 r1,0:150.64 1:150.65,A:2835225993;C:2589629327;G:2820499304;T:2931557102;N:67506,150,150,,,2835225993,2589629327,2820499304,2931557102,67506,SRX11248280,SRS9294818,SRA1251952,GEO,"ZMF, University Heidelberg",2,0.87724,0.87448,0.31729,0.31569,0.73716,0.73933,0.62206,0.62398,151,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2021-06-29,Undetermined,Multi-stage,Kidney,Renal System 65129,SRR14935650,SRX11248279,SRS9294817,SRP325966,PRJNA742218,Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing,GSE179104,Transcriptome Analysis,The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys,,pubmed:35100334,,kidney pdx1 heterozygous ko rep8,GSM5406801,,source name:total kidney|genotype:PDX1mut|tissue:kidney,kidney pdx1 heterozygous ko rep8,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,total kidney,,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,genotype:PDX1mut|tissue:kidney,GSM5406801,GSM5406801: kidney pdx1 heterozygous ko rep8; Danio rerio; RNA Seq,GSM5406801,,1,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM5406801,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP325966,,loader:fastq load.py,8724R1_17_R1_001.fastq.gz 8724R1_17_R2_001.fastq.gz,fastq fastq,11394814456.0,37822298.0,GSM5406801 r1,0:150.65 1:150.62,A:2870553528;C:2617084802;G:2858252766;T:3048861279;N:62081,150,150,,,2870553528,2617084802,2858252766,3048861279,62081,SRX11248279,SRS9294817,SRA1251952,GEO,"ZMF, University Heidelberg",2,0.88351,0.88116,0.29453,0.29339,0.72908,0.73012,0.59959,0.60047,151,151,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2021-06-29,Undetermined,Multi-stage,Kidney,Renal System 65130,SRR14935649,SRX11248278,SRS9294816,SRP325966,PRJNA742218,Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing,GSE179104,Transcriptome Analysis,The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys,,pubmed:35100334,,kidney pdx1 heterozygous ko rep7,GSM5406800,,source name:total kidney|genotype:PDX1mut|tissue:kidney,kidney pdx1 heterozygous ko rep7,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,total kidney,,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,genotype:PDX1mut|tissue:kidney,GSM5406800,GSM5406800: kidney pdx1 heterozygous ko rep7; Danio rerio; RNA Seq,GSM5406800,,1,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM5406800,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP325966,,loader:fastq load.py,8724R1_16_R1_001.fastq.gz 8724R1_16_R2_001.fastq.gz,fastq fastq,10795664046.0,35825557.0,GSM5406800 r1,0:150.66 1:150.68,A:2699673063;C:2430598463;G:2795587348;T:2869745840;N:59332,150,150,,,2699673063,2430598463,2795587348,2869745840,59332,SRX11248278,SRS9294816,SRA1251952,GEO,"ZMF, University Heidelberg",2,0.87086,0.8686,0.31803,0.31528,0.73517,0.73752,0.60984,0.61136,151,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2021-06-29,Undetermined,Multi-stage,Kidney,Renal System 65131,SRR14935648,SRX11248277,SRS9294815,SRP325966,PRJNA742218,Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing,GSE179104,Transcriptome Analysis,The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys,,pubmed:35100334,,kidney pdx1 heterozygous ko rep6,GSM5406799,,source name:total kidney|genotype:PDX1mut|tissue:kidney,kidney pdx1 heterozygous ko rep6,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,total kidney,,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,genotype:PDX1mut|tissue:kidney,GSM5406799,GSM5406799: kidney pdx1 heterozygous ko rep6; Danio rerio; RNA Seq,GSM5406799,,1,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM5406799,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP325966,,loader:fastq load.py,8724R1_15_R1_001.fastq.gz 8724R1_15_R2_001.fastq.gz,fastq fastq,10760871119.0,35714100.0,GSM5406799 r1,0:150.66 1:150.65,A:2739382001;C:2429434631;G:2669749643;T:2922244501;N:60343,150,150,,,2739382001,2429434631,2669749643,2922244501,60343,SRX11248277,SRS9294815,SRA1251952,GEO,"ZMF, University Heidelberg",2,0.8687,0.86692,0.3287,0.32779,0.73405,0.73486,0.60891,0.61291,151,150,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2021-06-29,Undetermined,Multi-stage,Kidney,Renal System 65132,SRR14935647,SRX11248276,SRS9294814,SRP325966,PRJNA742218,Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing,GSE179104,Transcriptome Analysis,The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys,,pubmed:35100334,,kidney pdx1 heterozygous ko rep5,GSM5406798,,source name:total kidney|genotype:PDX1mut|tissue:kidney,kidney pdx1 heterozygous ko rep5,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,total kidney,,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,genotype:PDX1mut|tissue:kidney,GSM5406798,GSM5406798: kidney pdx1 heterozygous ko rep5; Danio rerio; RNA Seq,GSM5406798,,1,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM5406798,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP325966,,loader:fastq load.py,8724R1_14_R1_001.fastq.gz 8724R1_14_R2_001.fastq.gz,fastq fastq,10649537104.0,35349599.0,GSM5406798 r1,0:150.64 1:150.62,A:2731221488;C:2409467117;G:2701711963;T:2807076164;N:60372,150,150,,,2731221488,2409467117,2701711963,2807076164,60372,SRX11248276,SRS9294814,SRA1251952,GEO,"ZMF, University Heidelberg",2,0.87441,0.87237,0.29421,0.29338,0.72693,0.72955,0.5953,0.59497,151,151,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2021-06-29,Undetermined,Multi-stage,Kidney,Renal System 65133,SRR14935646,SRX11248275,SRS9294813,SRP325966,PRJNA742218,Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing,GSE179104,Transcriptome Analysis,The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys,,pubmed:35100334,,kidney pdx1 heterozygous ko rep4,GSM5406797,,source name:total kidney|genotype:PDX1mut|tissue:kidney,kidney pdx1 heterozygous ko rep4,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,total kidney,,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,genotype:PDX1mut|tissue:kidney,GSM5406797,GSM5406797: kidney pdx1 heterozygous ko rep4; Danio rerio; RNA Seq,GSM5406797,,1,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM5406797,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP325966,,loader:fastq load.py,8724R1_13_R1_001.fastq.gz 8724R1_13_R2_001.fastq.gz,fastq fastq,10694204698.0,35493814.0,GSM5406797 r1,0:150.66 1:150.64,A:2702728213;C:2453895836;G:2650869868;T:2886649326;N:61455,150,150,,,2702728213,2453895836,2650869868,2886649326,61455,SRX11248275,SRS9294813,SRA1251952,GEO,"ZMF, University Heidelberg",2,0.87706,0.87455,0.30298,0.30085,0.73492,0.73499,0.60664,0.61545,149,151,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2021-06-29,Undetermined,Multi-stage,Kidney,Renal System 65134,SRR14935645,SRX11248274,SRS9294812,SRP325966,PRJNA742218,Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing,GSE179104,Transcriptome Analysis,The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys,,pubmed:35100334,,kidney pdx1 heterozygous ko rep3,GSM5406796,,source name:total kidney|genotype:PDX1mut|tissue:kidney,kidney pdx1 heterozygous ko rep3,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,total kidney,,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,genotype:PDX1mut|tissue:kidney,GSM5406796,GSM5406796: kidney pdx1 heterozygous ko rep3; Danio rerio; RNA Seq,GSM5406796,,1,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM5406796,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP325966,,loader:fastq load.py,8724R1_12_R1_001.fastq.gz 8724R1_12_R2_001.fastq.gz,fastq fastq,10345053183.0,34342254.0,GSM5406796 r1,0:150.63 1:150.60,A:2688355747;C:2362640622;G:2528888231;T:2765108367;N:60216,150,150,,,2688355747,2362640622,2528888231,2765108367,60216,SRX11248274,SRS9294812,SRA1251952,GEO,"ZMF, University Heidelberg",2,0.86578,0.86485,0.32858,0.32741,0.74022,0.74192,0.6202,0.62802,150,151,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2021-06-29,Undetermined,Multi-stage,Kidney,Renal System 65135,SRR14935644,SRX11248273,SRS9294811,SRP325966,PRJNA742218,Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing,GSE179104,Transcriptome Analysis,The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys,,pubmed:35100334,,kidney pdx1 heterozygous ko rep2,GSM5406795,,source name:total kidney|genotype:PDX1mut|tissue:kidney,kidney pdx1 heterozygous ko rep2,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,total kidney,,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,genotype:PDX1mut|tissue:kidney,GSM5406795,GSM5406795: kidney pdx1 heterozygous ko rep2; Danio rerio; RNA Seq,GSM5406795,,1,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM5406795,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP325966,,loader:fastq load.py,8724R1_11_R1_001.fastq.gz 8724R1_11_R2_001.fastq.gz,fastq fastq,10918902659.0,36232610.0,GSM5406795 r1,0:150.67 1:150.68,A:2720295545;C:2469360250;G:2821457214;T:2907726754;N:62896,150,150,,,2720295545,2469360250,2821457214,2907726754,62896,SRX11248273,SRS9294811,SRA1251952,GEO,"ZMF, University Heidelberg",2,0.87461,0.87362,0.33405,0.33405,0.74024,0.73994,0.60898,0.60832,151,151,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2021-06-29,Undetermined,Multi-stage,Kidney,Renal System 65136,SRR14935643,SRX11248272,SRS9294810,SRP325966,PRJNA742218,Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing,GSE179104,Transcriptome Analysis,The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys,,pubmed:35100334,,kidney pdx1 heterozygous ko rep1,GSM5406794,,source name:total kidney|genotype:PDX1mut|tissue:kidney,kidney pdx1 heterozygous ko rep1,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,total kidney,,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,genotype:PDX1mut|tissue:kidney,GSM5406794,GSM5406794: kidney pdx1 heterozygous ko rep1; Danio rerio; RNA Seq,GSM5406794,,1,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM5406794,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP325966,,loader:fastq load.py,8724R1_10_R1_001.fastq.gz 8724R1_10_R2_001.fastq.gz,fastq fastq,11557818156.0,38359672.0,GSM5406794 r1,0:150.63 1:150.67,A:2923769735;C:2594538133;G:2968671202;T:3070777088;N:61998,150,150,,,2923769735,2594538133,2968671202,3070777088,61998,SRX11248272,SRS9294810,SRA1251952,GEO,"ZMF, University Heidelberg",2,0.8705,0.86891,0.33241,0.3311,0.7363,0.73835,0.61699,0.62373,151,151,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2021-06-29,Undetermined,Multi-stage,Kidney,Renal System 65137,SRR14935642,SRX11248271,SRS9294809,SRP325966,PRJNA742218,Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing,GSE179104,Transcriptome Analysis,The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys,,pubmed:35100334,,kidney wildtype rep3,GSM5406793,,source name:total kidney|genotype:WT|tissue:kidney,kidney wildtype rep3,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,total kidney,,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,genotype:WT|tissue:kidney,GSM5406793,GSM5406793: kidney wildtype rep3; Danio rerio; RNA Seq,GSM5406793,,1,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM5406793,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP325966,,loader:fastq load.py,8724R1_3_R1_001.fastq.gz 8724R1_3_R2_001.fastq.gz,fastq fastq,10759333910.0,35709735.0,GSM5406793 r1,0:150.63 1:150.67,A:2742030248;C:2405074908;G:2740896620;T:2871268925;N:63209,150,150,,,2742030248,2405074908,2740896620,2871268925,63209,SRX11248271,SRS9294809,SRA1251952,GEO,"ZMF, University Heidelberg",2,0.87736,0.875,0.29165,0.29063,0.73261,0.73361,0.51754,0.51714,150,151,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2021-06-29,Undetermined,Multi-stage,Kidney,Renal System 65138,SRR14935641,SRX11248270,SRS9294808,SRP325966,PRJNA742218,Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing,GSE179104,Transcriptome Analysis,The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys,,pubmed:35100334,,kidney wildtype rep2,GSM5406792,,source name:total kidney|genotype:WT|tissue:kidney,kidney wildtype rep2,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,total kidney,,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,genotype:WT|tissue:kidney,GSM5406792,GSM5406792: kidney wildtype rep2; Danio rerio; RNA Seq,GSM5406792,,1,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM5406792,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP325966,,loader:fastq load.py,8724R1_2_R1_001.fastq.gz 8724R1_2_R2_001.fastq.gz,fastq fastq,11014631579.0,36552301.0,GSM5406792 r1,0:150.65 1:150.68,A:2786726244;C:2457413219;G:2801015846;T:2969414816;N:61454,150,150,,,2786726244,2457413219,2801015846,2969414816,61454,SRX11248270,SRS9294808,SRA1251952,GEO,"ZMF, University Heidelberg",2,0.87866,0.87699,0.31394,0.31278,0.73588,0.73726,0.61713,0.61801,151,151,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2021-06-29,Undetermined,Multi-stage,Kidney,Renal System 65139,SRR14935640,SRX11248269,SRS9294807,SRP325966,PRJNA742218,Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing,GSE179104,Transcriptome Analysis,The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys,,pubmed:35100334,,kidney wildtype rep1,GSM5406791,,source name:total kidney|genotype:WT|tissue:kidney,kidney wildtype rep1,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,total kidney,,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,genotype:WT|tissue:kidney,GSM5406791,GSM5406791: kidney wildtype rep1; Danio rerio; RNA Seq,GSM5406791,,1,Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,GEO Accession:GSM5406791,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP325966,,loader:fastq load.py,8724R1_1_R1_001.fastq.gz 8724R1_1_R2_001.fastq.gz,fastq fastq,10413411371.0,34567408.0,GSM5406791 r1,0:150.65 1:150.60,A:2697353558;C:2358512324;G:2568693377;T:2788789911;N:62201,150,150,,,2697353558,2358512324,2568693377,2788789911,62201,SRX11248269,SRS9294807,SRA1251952,GEO,"ZMF, University Heidelberg",2,0.86943,0.8664,0.31108,0.30889,0.73815,0.74034,0.56789,0.60471,151,151,B,B,biological fallback assumption,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2021-06-29,Undetermined,Multi-stage,Kidney,Renal System 66210,SRR16102702,SRX12388690,SRS10358692,SRP339154,PRJNA767083,RNA seq analysis for IRF4 driven zebrafish tumors post JQ1 treatment,GSE184946,Transcriptome Analysis,RNA seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes post JQ1 treatment Overall design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1 or control DMSO for 1 or 3 days. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells JQ1 day3 rep3 RNA Seq,GSM5602251,,tissue:Zebrafish tumor cells|cell type:Zebrafish tumor cells|condition:treatment|treatment:JQ1,Tumor cells JQ1 day3 rep3 RNA Seq,RNA seq datasets of DMSO treated control samples and JQ1 treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation. Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1 treated samples. Genome build: danRer11 Supplementary files format and content: featureCount read count for all sample DESeq2 files for differentially expressed genes,Zebrafish tumor cells,JQ1 was dissolved in DMSO. Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days. Experiments were done using 3 independent animals.,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,cell type:Zebrafish tumor cells|condition:treatment|treatment:JQ1,GSM5602251,GSM5602251: Tumor cells JQ1 day3 rep3 RNA Seq; Danio rerio; RNA Seq,GSM5602251,,1,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM5602251,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP339154,,,D3_J3_1.fq.gz D3_J3_2.fq.gz,fastq fastq,4552030000.0,45520300.0,GSM5602251 r1,0:100 1:100,A:1214627731;C:1045617960;G:1070259567;T:1221524742;N:0,100,100,,,1214627731,1045617960,1070259567,1221524742,0,SRX12388690,SRS10358692,SRA1302013,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.93576,,0.23142,,0.74144,,0.48177,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2021-09-28,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor 66211,SRR16102701,SRX12388689,SRS10358691,SRP339154,PRJNA767083,RNA seq analysis for IRF4 driven zebrafish tumors post JQ1 treatment,GSE184946,Transcriptome Analysis,RNA seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes post JQ1 treatment Overall design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1 or control DMSO for 1 or 3 days. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells JQ1 day3 rep2 RNA Seq,GSM5602250,,tissue:Zebrafish tumor cells|cell type:Zebrafish tumor cells|condition:treatment|treatment:JQ1,Tumor cells JQ1 day3 rep2 RNA Seq,RNA seq datasets of DMSO treated control samples and JQ1 treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation. Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1 treated samples. Genome build: danRer11 Supplementary files format and content: featureCount read count for all sample DESeq2 files for differentially expressed genes,Zebrafish tumor cells,JQ1 was dissolved in DMSO. Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days. Experiments were done using 3 independent animals.,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,cell type:Zebrafish tumor cells|condition:treatment|treatment:JQ1,GSM5602250,GSM5602250: Tumor cells JQ1 day3 rep2 RNA Seq; Danio rerio; RNA Seq,GSM5602250,,1,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM5602250,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP339154,,,D3_J2_1.fq.gz D3_J2_2.fq.gz,fastq fastq,4475915200.0,44759152.0,GSM5602250 r1,0:100 1:100,A:1189464447;C:1030660361;G:1055524478;T:1200265914;N:0,100,100,,,1189464447,1030660361,1055524478,1200265914,0,SRX12388689,SRS10358691,SRA1302013,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94062,,0.18735,,0.69759,,0.49542,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2021-09-28,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor 66212,SRR16102700,SRX12388688,SRS10358690,SRP339154,PRJNA767083,RNA seq analysis for IRF4 driven zebrafish tumors post JQ1 treatment,GSE184946,Transcriptome Analysis,RNA seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes post JQ1 treatment Overall design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1 or control DMSO for 1 or 3 days. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells JQ1 day3 rep1 RNA Seq,GSM5602249,,tissue:Zebrafish tumor cells|cell type:Zebrafish tumor cells|condition:treatment|treatment:JQ1,Tumor cells JQ1 day3 rep1 RNA Seq,RNA seq datasets of DMSO treated control samples and JQ1 treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation. Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1 treated samples. Genome build: danRer11 Supplementary files format and content: featureCount read count for all sample DESeq2 files for differentially expressed genes,Zebrafish tumor cells,JQ1 was dissolved in DMSO. Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days. Experiments were done using 3 independent animals.,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,cell type:Zebrafish tumor cells|condition:treatment|treatment:JQ1,GSM5602249,GSM5602249: Tumor cells JQ1 day3 rep1 RNA Seq; Danio rerio; RNA Seq,GSM5602249,,1,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM5602249,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP339154,,,D3_J1_1.fq.gz D3_J1_2.fq.gz,fastq fastq,4442146800.0,44421468.0,GSM5602249 r1,0:100 1:100,A:1179373951;C:1024313469;G:1050720604;T:1187738776;N:0,100,100,,,1179373951,1024313469,1050720604,1187738776,0,SRX12388688,SRS10358690,SRA1302013,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94195,,0.23006,,0.72894,,0.4972,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2021-09-28,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor 66213,SRR16102699,SRX12388687,SRS10358689,SRP339154,PRJNA767083,RNA seq analysis for IRF4 driven zebrafish tumors post JQ1 treatment,GSE184946,Transcriptome Analysis,RNA seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes post JQ1 treatment Overall design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1 or control DMSO for 1 or 3 days. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells DMSO day3 rep3 RNA Seq,GSM5602248,,tissue:Zebrafish tumor cells|cell type:Zebrafish tumor cells|condition:control|treatment:DMSO,Tumor cells DMSO day3 rep3 RNA Seq,RNA seq datasets of DMSO treated control samples and JQ1 treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation. Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1 treated samples. Genome build: danRer11 Supplementary files format and content: featureCount read count for all sample DESeq2 files for differentially expressed genes,Zebrafish tumor cells,JQ1 was dissolved in DMSO. Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days. Experiments were done using 3 independent animals.,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,cell type:Zebrafish tumor cells|condition:control|treatment:DMSO,GSM5602248,GSM5602248: Tumor cells DMSO day3 rep3 RNA Seq; Danio rerio; RNA Seq,GSM5602248,,1,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM5602248,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP339154,,,D3_D3_1.fq.gz D3_D3_2.fq.gz,fastq fastq,4446401600.0,44464016.0,GSM5602248 r1,0:100 1:100,A:1202900253;C:1006105416;G:1022157182;T:1215238749;N:0,100,100,,,1202900253,1006105416,1022157182,1215238749,0,SRX12388687,SRS10358689,SRA1302013,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.95301,,0.35614,,0.79961,,0.50405,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2021-09-28,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor 66214,SRR16102698,SRX12388686,SRS10358687,SRP339154,PRJNA767083,RNA seq analysis for IRF4 driven zebrafish tumors post JQ1 treatment,GSE184946,Transcriptome Analysis,RNA seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes post JQ1 treatment Overall design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1 or control DMSO for 1 or 3 days. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells DMSO day3 rep2 RNA Seq,GSM5602247,,tissue:Zebrafish tumor cells|cell type:Zebrafish tumor cells|condition:control|treatment:DMSO,Tumor cells DMSO day3 rep2 RNA Seq,RNA seq datasets of DMSO treated control samples and JQ1 treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation. Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1 treated samples. Genome build: danRer11 Supplementary files format and content: featureCount read count for all sample DESeq2 files for differentially expressed genes,Zebrafish tumor cells,JQ1 was dissolved in DMSO. Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days. Experiments were done using 3 independent animals.,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,cell type:Zebrafish tumor cells|condition:control|treatment:DMSO,GSM5602247,GSM5602247: Tumor cells DMSO day3 rep2 RNA Seq; Danio rerio; RNA Seq,GSM5602247,,1,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM5602247,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP339154,,,D3_D2_1.fq.gz D3_D2_2.fq.gz,fastq fastq,4459355600.0,44593556.0,GSM5602247 r1,0:100 1:100,A:1202802143;C:1015451294;G:1025320457;T:1215781706;N:0,100,100,,,1202802143,1015451294,1025320457,1215781706,0,SRX12388686,SRS10358687,SRA1302013,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.9443,,0.32993,,0.77786,,0.50186,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2021-09-28,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor 66215,SRR16102697,SRX12388685,SRS10358686,SRP339154,PRJNA767083,RNA seq analysis for IRF4 driven zebrafish tumors post JQ1 treatment,GSE184946,Transcriptome Analysis,RNA seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes post JQ1 treatment Overall design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1 or control DMSO for 1 or 3 days. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells DMSO day3 rep1 RNA Seq,GSM5602246,,tissue:Zebrafish tumor cells|cell type:Zebrafish tumor cells|condition:control|treatment:DMSO,Tumor cells DMSO day3 rep1 RNA Seq,RNA seq datasets of DMSO treated control samples and JQ1 treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation. Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1 treated samples. Genome build: danRer11 Supplementary files format and content: featureCount read count for all sample DESeq2 files for differentially expressed genes,Zebrafish tumor cells,JQ1 was dissolved in DMSO. Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days. Experiments were done using 3 independent animals.,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,cell type:Zebrafish tumor cells|condition:control|treatment:DMSO,GSM5602246,GSM5602246: Tumor cells DMSO day3 rep1 RNA Seq; Danio rerio; RNA Seq,GSM5602246,,1,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM5602246,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP339154,,,D3_D1_1.fq.gz D3_D1_2.fq.gz,fastq fastq,4486671200.0,44866712.0,GSM5602246 r1,0:100 1:100,A:1182551057;C:1045032741;G:1067880067;T:1191207335;N:0,100,100,,,1182551057,1045032741,1067880067,1191207335,0,SRX12388685,SRS10358686,SRA1302013,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94059,,0.21995,,0.76658,,0.47389,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2021-09-28,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor 66216,SRR16102696,SRX12388684,SRS10358685,SRP339154,PRJNA767083,RNA seq analysis for IRF4 driven zebrafish tumors post JQ1 treatment,GSE184946,Transcriptome Analysis,RNA seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes post JQ1 treatment Overall design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1 or control DMSO for 1 or 3 days. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells JQ1 day1 rep3 RNA Seq,GSM5602245,,tissue:Zebrafish tumor cells|cell type:Zebrafish tumor cells|condition:treatment|treatment:JQ1,Tumor cells JQ1 day1 rep3 RNA Seq,RNA seq datasets of DMSO treated control samples and JQ1 treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation. Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1 treated samples. Genome build: danRer11 Supplementary files format and content: featureCount read count for all sample DESeq2 files for differentially expressed genes,Zebrafish tumor cells,JQ1 was dissolved in DMSO. Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days. Experiments were done using 3 independent animals.,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,cell type:Zebrafish tumor cells|condition:treatment|treatment:JQ1,GSM5602245,GSM5602245: Tumor cells JQ1 day1 rep3 RNA Seq; Danio rerio; RNA Seq,GSM5602245,,1,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM5602245,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP339154,,,D1_J3_1.fq.gz D1_J3_2.fq.gz,fastq fastq,4550470000.0,45504700.0,GSM5602245 r1,0:100 1:100,A:1213052369;C:1047508174;G:1069309019;T:1220600438;N:0,100,100,,,1213052369,1047508174,1069309019,1220600438,0,SRX12388684,SRS10358685,SRA1302013,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94051,,0.24901,,0.74899,,0.50515,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2021-09-28,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor 66217,SRR16102695,SRX12388683,SRS10358684,SRP339154,PRJNA767083,RNA seq analysis for IRF4 driven zebrafish tumors post JQ1 treatment,GSE184946,Transcriptome Analysis,RNA seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes post JQ1 treatment Overall design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1 or control DMSO for 1 or 3 days. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells JQ1 day1 rep2 RNA Seq,GSM5602244,,tissue:Zebrafish tumor cells|cell type:Zebrafish tumor cells|condition:treatment|treatment:JQ1,Tumor cells JQ1 day1 rep2 RNA Seq,RNA seq datasets of DMSO treated control samples and JQ1 treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation. Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1 treated samples. Genome build: danRer11 Supplementary files format and content: featureCount read count for all sample DESeq2 files for differentially expressed genes,Zebrafish tumor cells,JQ1 was dissolved in DMSO. Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days. Experiments were done using 3 independent animals.,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,cell type:Zebrafish tumor cells|condition:treatment|treatment:JQ1,GSM5602244,GSM5602244: Tumor cells JQ1 day1 rep2 RNA Seq; Danio rerio; RNA Seq,GSM5602244,,1,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM5602244,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP339154,,,D1_J2_1.fq.gz D1_J2_2.fq.gz,fastq fastq,4490144800.0,44901448.0,GSM5602244 r1,0:100 1:100,A:1197596235;C:1031109315;G:1057301946;T:1204137304;N:0,100,100,,,1197596235,1031109315,1057301946,1204137304,0,SRX12388683,SRS10358684,SRA1302013,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94477,,0.24522,,0.74042,,0.51025,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2021-09-28,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor 66218,SRR16102694,SRX12388682,SRS10358688,SRP339154,PRJNA767083,RNA seq analysis for IRF4 driven zebrafish tumors post JQ1 treatment,GSE184946,Transcriptome Analysis,RNA seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes post JQ1 treatment Overall design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1 or control DMSO for 1 or 3 days. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells JQ1 day1 rep1 RNA Seq,GSM5602243,,tissue:Zebrafish tumor cells|cell type:Zebrafish tumor cells|condition:treatment|treatment:JQ1,Tumor cells JQ1 day1 rep1 RNA Seq,RNA seq datasets of DMSO treated control samples and JQ1 treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation. Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1 treated samples. Genome build: danRer11 Supplementary files format and content: featureCount read count for all sample DESeq2 files for differentially expressed genes,Zebrafish tumor cells,JQ1 was dissolved in DMSO. Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days. Experiments were done using 3 independent animals.,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,cell type:Zebrafish tumor cells|condition:treatment|treatment:JQ1,GSM5602243,GSM5602243: Tumor cells JQ1 day1 rep1 RNA Seq; Danio rerio; RNA Seq,GSM5602243,,1,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM5602243,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP339154,,,D1_J1_1.fq.gz D1_J1_2.fq.gz,fastq fastq,4434887800.0,44348878.0,GSM5602243 r1,0:100 1:100,A:1178050199;C:1024865996;G:1046777721;T:1185193884;N:0,100,100,,,1178050199,1024865996,1046777721,1185193884,0,SRX12388682,SRS10358688,SRA1302013,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94501,,0.2305,,0.76432,,0.49472,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2021-09-28,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor 66219,SRR16102693,SRX12388681,SRS10358683,SRP339154,PRJNA767083,RNA seq analysis for IRF4 driven zebrafish tumors post JQ1 treatment,GSE184946,Transcriptome Analysis,RNA seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes post JQ1 treatment Overall design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1 or control DMSO for 1 or 3 days. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells DMSO day1 rep3 RNA Seq,GSM5602242,,tissue:Zebrafish tumor cells|cell type:Zebrafish tumor cells|condition:control|treatment:DMSO,Tumor cells DMSO day1 rep3 RNA Seq,RNA seq datasets of DMSO treated control samples and JQ1 treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation. Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1 treated samples. Genome build: danRer11 Supplementary files format and content: featureCount read count for all sample DESeq2 files for differentially expressed genes,Zebrafish tumor cells,JQ1 was dissolved in DMSO. Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days. Experiments were done using 3 independent animals.,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,cell type:Zebrafish tumor cells|condition:control|treatment:DMSO,GSM5602242,GSM5602242: Tumor cells DMSO day1 rep3 RNA Seq; Danio rerio; RNA Seq,GSM5602242,,1,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM5602242,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP339154,,,D1_D3_1.fq.gz D1_D3_2.fq.gz,fastq fastq,4497882800.0,44978828.0,GSM5602242 r1,0:100 1:100,A:1193693228;C:1038160916;G:1064460652;T:1201568004;N:0,100,100,,,1193693228,1038160916,1064460652,1201568004,0,SRX12388681,SRS10358683,SRA1302013,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.93714,,0.19697,,0.74554,,0.50928,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2021-09-28,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor 66220,SRR16102692,SRX12388680,SRS10358682,SRP339154,PRJNA767083,RNA seq analysis for IRF4 driven zebrafish tumors post JQ1 treatment,GSE184946,Transcriptome Analysis,RNA seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes post JQ1 treatment Overall design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1 or control DMSO for 1 or 3 days. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells DMSO day1 rep2 RNA Seq,GSM5602241,,tissue:Zebrafish tumor cells|cell type:Zebrafish tumor cells|condition:control|treatment:DMSO,Tumor cells DMSO day1 rep2 RNA Seq,RNA seq datasets of DMSO treated control samples and JQ1 treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation. Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1 treated samples. Genome build: danRer11 Supplementary files format and content: featureCount read count for all sample DESeq2 files for differentially expressed genes,Zebrafish tumor cells,JQ1 was dissolved in DMSO. Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days. Experiments were done using 3 independent animals.,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,cell type:Zebrafish tumor cells|condition:control|treatment:DMSO,GSM5602241,GSM5602241: Tumor cells DMSO day1 rep2 RNA Seq; Danio rerio; RNA Seq,GSM5602241,,1,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM5602241,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP339154,,,D1_D2_1.fq.gz D1_D2_2.fq.gz,fastq fastq,4464096200.0,44640962.0,GSM5602241 r1,0:100 1:100,A:1185692334;C:1031585570;G:1050205768;T:1196612528;N:0,100,100,,,1185692334,1031585570,1050205768,1196612528,0,SRX12388680,SRS10358682,SRA1302013,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94785,,0.24425,,0.78165,,0.4975,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2021-09-28,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor 66221,SRR16102691,SRX12388679,SRS10358681,SRP339154,PRJNA767083,RNA seq analysis for IRF4 driven zebrafish tumors post JQ1 treatment,GSE184946,Transcriptome Analysis,RNA seq analysis was performed using tumor cells driven by IRF4 to analyze gene expression changes post JQ1 treatment Overall design: The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1 or control DMSO for 1 or 3 days. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,parent bioproject:PRJNA701471,pubmed:35504924,,Tumor cells DMSO day1 rep1 RNA Seq,GSM5602240,,tissue:Zebrafish tumor cells|cell type:Zebrafish tumor cells|condition:control|treatment:DMSO,Tumor cells DMSO day1 rep1 RNA Seq,RNA seq datasets of DMSO treated control samples and JQ1 treated samples were aligned to the GRCz11 zebrafish genome Ensembl annotation with ERCC spike in information using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1. featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation and ERCC annotation. Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 3 DMSO vs 3 JQ1 treated samples. Genome build: danRer11 Supplementary files format and content: featureCount read count for all sample DESeq2 files for differentially expressed genes,Zebrafish tumor cells,JQ1 was dissolved in DMSO. Animals were treated with JQ1 at 4microM or the same amount of DMSO in individual tanks for 1 or 3 days. Experiments were done using 3 independent animals.,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,The human IRF4 gene and mCherry fluorescent marker gene were transduced under the zebrafish lck promoter in zebrafish. post the development of lymphoma phenotype animals were treated with JQ1. Tumor cells were harvested and sorted by flow cytometry based on mCherry fluorescence expression. Total RNAs were harvested from each sample and then applied for RNA seq analysis.,cell type:Zebrafish tumor cells|condition:control|treatment:DMSO,GSM5602240,GSM5602240: Tumor cells DMSO day1 rep1 RNA Seq; Danio rerio; RNA Seq,GSM5602240,,1,Total RNA was harvested using the miRNeasy Mini Kit Qiagen. ERCC spike in was added based on the total cell number. Strand specific library construction and sequencing of paired end 100 bp long reads by the BGISeq500 were performed at the BGI Biotech Solutions Hong Kong Co Ltd Hong Kong.,GEO Accession:GSM5602240,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP339154,,,D1_D1_1.fq.gz D1_D1_2.fq.gz,fastq fastq,4466502200.0,44665022.0,GSM5602240 r1,0:100 1:100,A:1191785539;C:1024344626;G:1050598581;T:1199773454;N:0,100,100,,,1191785539,1024344626,1050598581,1199773454,0,SRX12388679,SRS10358681,SRA1302013,GEO,"Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore",1,0.94073,,0.24308,,0.77094,,0.48493,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Singapore,2021-09-28,Undetermined,Undetermined,Cancer or Tumor,Cancer or Tumor 70080,SRR19445938,SRX15499122,SRS13214006,SRP377632,PRJNA843695,Loss of Glo2 alters the glucose metabolism in zebrafish,GSE205085,Transcriptome Analysis,Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.,,pubmed:36535130,,Glo2 / 6,GSM6205029,,source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:KO,Glo2 / 6,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,Tgfli1:EGFP,,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:whole liver|trained:no|genotype:KO,GSM6205029,GSM6205029: Glo2 / 6; Danio rerio; RNA Seq,GSM6205029 r1,GSM6205029,1,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP377632,,,12.1_1.fq.gz 12.1_2.fq.gz,fastq fastq,4163038200.0,41630382.0,GSM6205029 r1,0:100 1:100,A:1080428167;C:982538284;G:1004098821;T:1095972928;N:0,100,100,,,1080428167,982538284,1004098821,1095972928,0,SRX15499122,SRS13214006,SRA1428824,"ZMF, University Heidelberg","ZMF, University Heidelberg",1,0.95934,,0.04773,,0.80028,,0.52892,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2022-05-30,Undetermined,Larval,Liver,Liver and Biliary System 70081,SRR19445939,SRX15499121,SRS13214005,SRP377632,PRJNA843695,Loss of Glo2 alters the glucose metabolism in zebrafish,GSE205085,Transcriptome Analysis,Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.,,pubmed:36535130,,Glo2 +/+ 6,GSM6205028,,source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:WT,Glo2 +/+ 6,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,Tgfli1:EGFP,,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:whole liver|trained:no|genotype:WT,GSM6205028,GSM6205028: Glo2 +/+ 6; Danio rerio; RNA Seq,GSM6205028 r1,GSM6205028,1,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP377632,,,11.1_1.fq.gz 11.1_2.fq.gz,fastq fastq,4170292600.0,41702926.0,GSM6205028 r1,0:100 1:100,A:1081431596;C:983791100;G:1012532071;T:1092537833;N:0,100,100,,,1081431596,983791100,1012532071,1092537833,0,SRX15499121,SRS13214005,SRA1428824,"ZMF, University Heidelberg","ZMF, University Heidelberg",1,0.95587,,0.0499,,0.80805,,0.50421,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2022-05-30,Undetermined,Larval,Liver,Liver and Biliary System 70082,SRR19445940,SRX15499120,SRS13214004,SRP377632,PRJNA843695,Loss of Glo2 alters the glucose metabolism in zebrafish,GSE205085,Transcriptome Analysis,Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.,,pubmed:36535130,,Glo2 / 5,GSM6205027,,source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:KO,Glo2 / 5,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,Tgfli1:EGFP,,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:whole liver|trained:no|genotype:KO,GSM6205027,GSM6205027: Glo2 / 5; Danio rerio; RNA Seq,GSM6205027 r1,GSM6205027,1,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP377632,,,10.1_1.fq.gz 10.1_2.fq.gz,fastq fastq,4165964600.0,41659646.0,GSM6205027 r1,0:100 1:100,A:1087548367;C:975174787;G:1002623835;T:1100617611;N:0,100,100,,,1087548367,975174787,1002623835,1100617611,0,SRX15499120,SRS13214004,SRA1428824,"ZMF, University Heidelberg","ZMF, University Heidelberg",1,0.95351,,0.05573,,0.80229,,0.5231,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2022-05-30,Undetermined,Larval,Liver,Liver and Biliary System 70083,SRR19445941,SRX15499119,SRS13214003,SRP377632,PRJNA843695,Loss of Glo2 alters the glucose metabolism in zebrafish,GSE205085,Transcriptome Analysis,Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.,,pubmed:36535130,,Glo2 +/+ 5,GSM6205026,,source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:WT,Glo2 +/+ 5,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,Tgfli1:EGFP,,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:whole liver|trained:no|genotype:WT,GSM6205026,GSM6205026: Glo2 +/+ 5; Danio rerio; RNA Seq,GSM6205026 r1,GSM6205026,1,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP377632,,,9.1_1.fq.gz 9.1_2.fq.gz,fastq fastq,4161803400.0,41618034.0,GSM6205026 r1,0:100 1:100,A:1084378904;C:978685192;G:1004569873;T:1094169431;N:0,100,100,,,1084378904,978685192,1004569873,1094169431,0,SRX15499119,SRS13214003,SRA1428824,"ZMF, University Heidelberg","ZMF, University Heidelberg",1,0.95218,,0.04867,,0.80732,,0.52859,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2022-05-30,Undetermined,Larval,Liver,Liver and Biliary System 70084,SRR19445942,SRX15499118,SRS13214002,SRP377632,PRJNA843695,Loss of Glo2 alters the glucose metabolism in zebrafish,GSE205085,Transcriptome Analysis,Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.,,pubmed:36535130,,Glo2 / 4,GSM6205025,,source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:KO,Glo2 / 4,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,Tgfli1:EGFP,,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:whole liver|trained:no|genotype:KO,GSM6205025,GSM6205025: Glo2 / 4; Danio rerio; RNA Seq,GSM6205025 r1,GSM6205025,1,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP377632,,,8.1_1.fq.gz 8.1_2.fq.gz,fastq fastq,4152089400.0,41520894.0,GSM6205025 r1,0:100 1:100,A:1071439906;C:981252736;G:1021757559;T:1077639199;N:0,100,100,,,1071439906,981252736,1021757559,1077639199,0,SRX15499118,SRS13214002,SRA1428824,"ZMF, University Heidelberg","ZMF, University Heidelberg",1,0.94509,,0.04233,,0.82031,,0.5193,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2022-05-30,Undetermined,Larval,Liver,Liver and Biliary System 70085,SRR19445943,SRX15499117,SRS13214001,SRP377632,PRJNA843695,Loss of Glo2 alters the glucose metabolism in zebrafish,GSE205085,Transcriptome Analysis,Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.,,pubmed:36535130,,Glo2 +/+ 4,GSM6205024,,source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:WT,Glo2 +/+ 4,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,Tgfli1:EGFP,,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:whole liver|trained:no|genotype:WT,GSM6205024,GSM6205024: Glo2 +/+ 4; Danio rerio; RNA Seq,GSM6205024 r1,GSM6205024,1,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP377632,,,7.1_1.fq.gz 7.1_2.fq.gz,fastq fastq,4164307200.0,41643072.0,GSM6205024 r1,0:100 1:100,A:1089101337;C:971144234;G:1001055993;T:1103005636;N:0,100,100,,,1089101337,971144234,1001055993,1103005636,0,SRX15499117,SRS13214001,SRA1428824,"ZMF, University Heidelberg","ZMF, University Heidelberg",1,0.95715,,0.05232,,0.8062,,0.52299,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2022-05-30,Undetermined,Larval,Liver,Liver and Biliary System 70086,SRR19445944,SRX15499116,SRS13214000,SRP377632,PRJNA843695,Loss of Glo2 alters the glucose metabolism in zebrafish,GSE205085,Transcriptome Analysis,Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.,,pubmed:36535130,,Glo2 / 3,GSM6205023,,source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:KO,Glo2 / 3,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,Tgfli1:EGFP,,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:whole liver|trained:no|genotype:KO,GSM6205023,GSM6205023: Glo2 / 3; Danio rerio; RNA Seq,GSM6205023 r1,GSM6205023,1,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP377632,,,6.1_1.fq.gz 6.1_2.fq.gz,fastq fastq,4160202200.0,41602022.0,GSM6205023 r1,0:100 1:100,A:1078397784;C:984320163;G:1006828922;T:1090655331;N:0,100,100,,,1078397784,984320163,1006828922,1090655331,0,SRX15499116,SRS13214000,SRA1428824,"ZMF, University Heidelberg","ZMF, University Heidelberg",1,0.95752,,0.04539,,0.8072,,0.5241,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2022-05-30,Undetermined,Larval,Liver,Liver and Biliary System 70087,SRR19445945,SRX15499115,SRS13213999,SRP377632,PRJNA843695,Loss of Glo2 alters the glucose metabolism in zebrafish,GSE205085,Transcriptome Analysis,Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.,,pubmed:36535130,,Glo2 +/+ 3,GSM6205022,,source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:WT,Glo2 +/+ 3,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,Tgfli1:EGFP,,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:whole liver|trained:no|genotype:WT,GSM6205022,GSM6205022: Glo2 +/+ 3; Danio rerio; RNA Seq,GSM6205022 r1,GSM6205022,1,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP377632,,,5.1_1.fq.gz 5.1_2.fq.gz,fastq fastq,4165235600.0,41652356.0,GSM6205022 r1,0:100 1:100,A:1072104475;C:989511105;G:1023359503;T:1080260517;N:0,100,100,,,1072104475,989511105,1023359503,1080260517,0,SRX15499115,SRS13213999,SRA1428824,"ZMF, University Heidelberg","ZMF, University Heidelberg",1,0.95194,,0.03798,,0.82087,,0.54781,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2022-05-30,Undetermined,Larval,Liver,Liver and Biliary System 70088,SRR19445946,SRX15499114,SRS13213998,SRP377632,PRJNA843695,Loss of Glo2 alters the glucose metabolism in zebrafish,GSE205085,Transcriptome Analysis,Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.,,pubmed:36535130,,Glo2 / 2,GSM6205021,,source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:KO,Glo2 / 2,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,Tgfli1:EGFP,,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:whole liver|trained:no|genotype:KO,GSM6205021,GSM6205021: Glo2 / 2; Danio rerio; RNA Seq,GSM6205021 r1,GSM6205021,1,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP377632,,,4.1_1.fq.gz 4.1_2.fq.gz,fastq fastq,4171018400.0,41710184.0,GSM6205021 r1,0:100 1:100,A:1073769040;C:990042636;G:1019695979;T:1087510745;N:0,100,100,,,1073769040,990042636,1019695979,1087510745,0,SRX15499114,SRS13213998,SRA1428824,"ZMF, University Heidelberg","ZMF, University Heidelberg",1,0.95183,,0.04539,,0.81134,,0.51505,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2022-05-30,Undetermined,Larval,Liver,Liver and Biliary System 70089,SRR19445947,SRX15499113,SRS13213997,SRP377632,PRJNA843695,Loss of Glo2 alters the glucose metabolism in zebrafish,GSE205085,Transcriptome Analysis,Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.,,pubmed:36535130,,Glo2 +/+ 2,GSM6205020,,source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:WT,Glo2 +/+ 2,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,Tgfli1:EGFP,,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:whole liver|trained:no|genotype:WT,GSM6205020,GSM6205020: Glo2 +/+ 2; Danio rerio; RNA Seq,GSM6205020 r1,GSM6205020,1,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP377632,,,3.1_1.fq.gz 3.1_2.fq.gz,fastq fastq,4145841000.0,41458410.0,GSM6205020 r1,0:100 1:100,A:1051425067;C:998554505;G:1029593084;T:1066268344;N:0,100,100,,,1051425067,998554505,1029593084,1066268344,0,SRX15499113,SRS13213997,SRA1428824,"ZMF, University Heidelberg","ZMF, University Heidelberg",1,0.96363,,0.03563,,0.81994,,0.49336,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2022-05-30,Undetermined,Larval,Liver,Liver and Biliary System 70090,SRR19445948,SRX15499112,SRS13213996,SRP377632,PRJNA843695,Loss of Glo2 alters the glucose metabolism in zebrafish,GSE205085,Transcriptome Analysis,Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.,,pubmed:36535130,,Glo2 / 1,GSM6205019,,source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:KO,Glo2 / 1,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,Tgfli1:EGFP,,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:whole liver|trained:no|genotype:KO,GSM6205019,GSM6205019: Glo2 / 1; Danio rerio; RNA Seq,GSM6205019 r1,GSM6205019,1,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP377632,,,2.1_1.fq.gz 2.1_2.fq.gz,fastq fastq,4147644400.0,41476444.0,GSM6205019 r1,0:100 1:100,A:1103014496;C:947498522;G:988532296;T:1108599086;N:0,100,100,,,1103014496,947498522,988532296,1108599086,0,SRX15499112,SRS13213996,SRA1428824,"ZMF, University Heidelberg","ZMF, University Heidelberg",1,0.94203,,0.05616,,0.81268,,0.5326,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2022-05-30,Undetermined,Larval,Liver,Liver and Biliary System 70091,SRR19445949,SRX15499111,SRS13213995,SRP377632,PRJNA843695,Loss of Glo2 alters the glucose metabolism in zebrafish,GSE205085,Transcriptome Analysis,Glyoxalase 2 is the second enzyme of the glyoxalase system catalyzing the detoxification of methylglyoxal to D lactate via SD Lactoylglutathione. Recent studies have suggested Glo2 as a regulator of glycolysis but the physiological functions of Glo2 in vivo and organ specific functions of the enzyme have not yet been evaluated. Therefore a CRISPR/Cas9 knockout of glo2 in zebrafish was created and analyzed. Consistent with its function in methylglyoxal detoxification SD Lactoylglutathione but not methylglyoxal accumulated in glo2 / larvae with no change in longevity. Adult glo2 / livers developed an impaired insulin signaling indicated by a reduced hepatic P70 S6 kinase activation and reduced hepatic hexose concentration. In contrast glo2 / skeletal muscle remained functionally intact compensating for the dysfunctional liver through increased glucose uptake thereby maintaining euglycemia and preventing damage of the retina and kidney. In conclusion the data identified Glo2 to fulfill similar but unique functions compared to Glo1 and established Glo2 as a novel target in diabetes research regulating hepatic insulin signaling. Overall design: A CRISPR based knockout of Glyoxalase 2 was created in zebrafish. The development of the fish was analyzed as well as organ specific glucose metabolism in skeletal muscle and liver. Imaging studies of Retina kidney liver and skeletal muscle were conducted. RNA sequencing was performed on adult liver tissue of glo2+/+ and glo2 / fish by BGI in collaboration with the NGS Core facility in Mannheim University of Heidelberg.,,pubmed:36535130,,Glo2 +/+ 1,GSM6205018,,source name:Tgfli1:EGFP|tissue:whole liver|trained:no|genotype:WT,Glo2 +/+ 1,trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Assembly: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto.,Tgfli1:EGFP,,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,tissue:whole liver|trained:no|genotype:WT,GSM6205018,GSM6205018: Glo2 +/+ 1; Danio rerio; RNA Seq,GSM6205018 r1,GSM6205018,1,Total RNA was extracted using TRIzol method RNA libraries were prepared for sequencing using standard BGISeq 500 protocols,,RNA-Seq,TRANSCRIPTOMIC,cDNA,PAIRED,BGISEQ,BGISEQ-500,,SRP377632,,,1.1_1.fq.gz 1.1_2.fq.gz,fastq fastq,4155343800.0,41553438.0,GSM6205018 r1,0:100 1:100,A:1072547817;C:985284919;G:1008557411;T:1088953653;N:0,100,100,,,1072547817,985284919,1008557411,1088953653,0,SRX15499111,SRS13213995,SRA1428824,"ZMF, University Heidelberg","ZMF, University Heidelberg",1,0.96135,,0.04666,,0.80543,,0.51213,,100,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Germany,2022-05-30,Undetermined,Larval,Liver,Liver and Biliary System 74613,SRR23868264,SRX19680348,SRS17049789,SRP427394,PRJNA944944,Comparative transcriptome analysis of testes and ovaries reveals sex biased genes and pathways in zebrafish,GSE227389,Transcriptome Analysis,The goals of this study are to compare the differentially expressed genes between testes and ovaries of zebrafish based on RNA seq data and some of these genes were validated by qRT–PCR.Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Testes and ovaries mRNA profiles of adult zebrafish were generated by deep sequencing. Every sample was compose of three adult individuals.,,pubmed:38242380,,testes,GSM7099751,,source name:testis|tissue:testis|genotype:WT|geo loc name:missing|collection date:missing,testes,Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Assembly: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample.,testis,,Testes and ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.,,tissue:testis|genotype:WT,GSM7099751,GSM7099751: testes; Danio rerio; RNA Seq,GSM7099751 r1,GSM7099751,1,Testes and ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP427394,,,WT-testis.fq.gz,fastq,1176068400.0,23521368.0,GSM7099751 r1,0:50,A:323799672;C:262049848;G:273563529;T:316045968;N:609383,50,,,,323799672,262049848,273563529,316045968,609383,SRX19680348,SRS17049789,SRA1687194,Wuhan university,Wuhan university,1,0.93023,,0.11308,,0.6462,,0.49784,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-03-15,Undetermined,Undetermined,Gonad,Reproductive System 74614,SRR23868265,SRX19680347,SRS17049788,SRP427394,PRJNA944944,Comparative transcriptome analysis of testes and ovaries reveals sex biased genes and pathways in zebrafish,GSE227389,Transcriptome Analysis,The goals of this study are to compare the differentially expressed genes between testes and ovaries of zebrafish based on RNA seq data and some of these genes were validated by qRT–PCR.Further the differentially expressed genes were devided into up regulated and down regulated genes for GO and KEGG analysis. Overall design: Testes and ovaries mRNA profiles of adult zebrafish were generated by deep sequencing. Every sample was compose of three adult individuals.,,pubmed:38242380,,ovaries,GSM7099752,,source name:ovary|tissue:ovary|genotype:WT|geo loc name:missing|collection date:missing,ovaries,Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz10 whole genome using HISAT mapped to genes using Bowtie2. fragments per kilo bases per million fragments FPKM were calculated using RSEM. Assembly: GRCz10 Supplementary files format and content: The text files include the Ensembl ID of genes and the FPKM values for each Sample.,ovary,,Testes and ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.,,tissue:ovary|genotype:WT,GSM7099752,GSM7099752: ovaries; Danio rerio; RNA Seq,GSM7099752 r1,GSM7099752,1,Testes and ovaries were isolated frozen on dry ice and RNA was harvested using Trizol reagent. Agilent RNA 6000 nano Reagents Port 1 was used for RNA qualities analysis by Agilent 2100 Bioanalyzer. RNA libraries were prepared for sequencing using standard BGISEQ 500 protocols.,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,BGISEQ,BGISEQ-500,,SRP427394,,,WT-ovary.fq.gz,fastq,1176463600.0,23529272.0,GSM7099752 r1,0:50,A:311869864;C:270650722;G:289863261;T:303489229;N:590524,50,,,,311869864,270650722,289863261,303489229,590524,SRX19680347,SRS17049788,SRA1687194,Wuhan university,Wuhan university,1,0.93488,,0.02755,,0.75601,,0.46986,,50,,B,,usable mapping rate,bgi,bgi,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,China,2023-03-15,Undetermined,Undetermined,Gonad,Reproductive System