{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Undetermined\" and experiment.platform = \"BGISEQ\"", "rows": [[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.", null, null, null, "pikfyve3", "GSM7883488", null, "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 \u2264 0.05 or FDR \u2264 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 \u2264 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", null, "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", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP470412", null, null, "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, null, null, 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", null, "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.", null, null, null, "pikfyve2", "GSM7883487", null, "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 \u2264 0.05 or FDR \u2264 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 \u2264 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", null, "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", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP470412", null, null, "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, null, null, 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", null, "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.", null, null, null, "pikfyve1", "GSM7883486", null, "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 \u2264 0.05 or FDR \u2264 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 \u2264 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", null, "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", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP470412", null, null, "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, null, null, 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", null, "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.", null, null, null, "WT3", "GSM7883485", null, "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 \u2264 0.05 or FDR \u2264 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 \u2264 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", null, "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", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP470412", null, null, "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, null, null, 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", null, "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.", null, null, null, "WT2", "GSM7883484", null, "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 \u2264 0.05 or FDR \u2264 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 \u2264 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", null, "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", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP470412", null, null, "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, null, null, 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", null, "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.", null, null, null, "WT1", "GSM7883483", null, "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 \u2264 0.05 or FDR \u2264 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 \u2264 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", null, "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", null, "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", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP470412", null, null, "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, null, null, 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", null, "China", "2023-11-06", "Undetermined", "Undetermined", "Undetermined", "Undetermined"], [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.", null, "pubmed:35504924", null, "IRF4 overexpression with p53 mutation RNA seq #2", "GSM4134351", null, "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", null, "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", null, "SRP226571", null, null, "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, null, null, 2336303355, 1960332457, 1974896588, 2376162876, 0, "SRX7032952", "SRS5553012", "SRA982884", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94146, null, 0.26739, null, 0.77739, null, 0.49821, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35504924", null, "IRF4 overexpression with p53 mutation RNA seq #1", "GSM4134350", null, "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", null, "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", null, "SRP226571", null, null, "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, null, null, 2293476693, 1963039176, 1985578185, 2337373998, 0, "SRX7032951", "SRS5553011", "SRA982884", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94576, null, 0.27683, null, 0.77589, null, 0.47851, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35504924", null, "IRF4 overexpression RNA seq #2", "GSM4134349", null, "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", null, "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", null, "SRP226571", null, null, "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, null, null, 2345513123, 1941948054, 1962855201, 2375093048, 0, "SRX7032950", "SRS5553010", "SRA982884", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94815, null, 0.35561, null, 0.79117, null, 0.50866, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35504924", null, "IRF4 overexpression RNA seq #1", "GSM4134348", null, "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", null, "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", null, "SRP226571", null, null, "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, null, null, 2300488079, 1940898245, 1978951452, 2339950840, 0, "SRX7032949", "SRS5553009", "SRA982884", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94019, null, 0.24387, null, 0.75789, null, 0.49007, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35504924", null, "mCherry control RNA seq #2", "GSM4134347", null, "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", null, "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", null, "SRP226571", null, null, "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, null, null, 2299427498, 1945648999, 1981590842, 2329900967, 0, "SRX7032948", "SRS5553008", "SRA982884", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94792, null, 0.25274, null, 0.80085, null, 0.51772, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:35504924", null, "mCherry control RNA seq #1", "GSM4134346", null, "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", null, "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", null, "SRP226571", null, null, "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, null, null, 2294044731, 1942271608, 1967598065, 2340304420, 0, "SRX7032947", "SRS5553007", "SRA982884", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94337, null, 0.28212, null, 0.79239, null, 0.47106, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2019-10-22", "Undetermined", "Undetermined", "Multi-tissue", "Multi-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.", null, "pubmed:33408418", null, "high Erk activity; rep1", "GSM4433141", null, "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 \u00b5m 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 \u2013 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 \u00b5l 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 \u00b5l of supernatant was removed  quenched with 65\u00b5l sheep serum Sigma S2263 on ice  and 500 \u00b5l of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 \u00b5l filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 \u00b5g/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", null, "1", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "GEO Accession:GSM4433141", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP254053", null, null, "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, null, null, 1261622105, 1085007643, 1066886112, 1285079340, 0, "SRX8003661", "SRS6377641", "SRA1059429", "GEO", "Poss, Cell Biology, Duke University", 1, 0.86576, null, 0.11767, null, 0.81262, null, 0.52377, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:33408418", null, "low Erk activity; rep3", "GSM4433140", null, "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 \u00b5m 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 \u2013 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 \u00b5l 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 \u00b5l of supernatant was removed  quenched with 65\u00b5l sheep serum Sigma S2263 on ice  and 500 \u00b5l of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 \u00b5l filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 \u00b5g/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", null, "1", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "GEO Accession:GSM4433140", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP254053", null, null, "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, null, null, 1268188059, 1086056259, 1067448053, 1285524629, 0, "SRX8003660", "SRS6377640", "SRA1059429", "GEO", "Poss, Cell Biology, Duke University", 1, 0.88883, null, 0.05585, null, 0.82071, null, 0.47905, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:33408418", null, "low Erk activity; rep2", "GSM4433139", null, "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 \u00b5m 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 \u2013 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 \u00b5l 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 \u00b5l of supernatant was removed  quenched with 65\u00b5l sheep serum Sigma S2263 on ice  and 500 \u00b5l of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 \u00b5l filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 \u00b5g/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", null, "1", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "GEO Accession:GSM4433139", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP254053", null, null, "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, null, null, 1240779500, 1112511484, 1096653049, 1255351567, 0, "SRX8003659", "SRS6377639", "SRA1059429", "GEO", "Poss, Cell Biology, Duke University", 1, 0.89254, null, 0.04065, null, 0.81197, null, 0.46307, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:33408418", null, "low Erk activity; rep1", "GSM4433138", null, "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 \u00b5m 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 \u2013 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 \u00b5l 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 \u00b5l of supernatant was removed  quenched with 65\u00b5l sheep serum Sigma S2263 on ice  and 500 \u00b5l of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 \u00b5l filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 \u00b5g/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", null, "1", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "GEO Accession:GSM4433138", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP254053", null, null, "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, null, null, 1275040914, 1077730597, 1059242617, 1295769272, 0, "SRX8003658", "SRS6377638", "SRA1059429", "GEO", "Poss, Cell Biology, Duke University", 1, 0.8629, null, 0.13994, null, 0.7838, null, 0.50568, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:33408418", null, "high Erk activity; rep3", "GSM4433143", null, "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 \u00b5m 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 \u2013 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 \u00b5l 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 \u00b5l of supernatant was removed  quenched with 65\u00b5l sheep serum Sigma S2263 on ice  and 500 \u00b5l of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 \u00b5l filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 \u00b5g/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", null, "1", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "GEO Accession:GSM4433143", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP254053", null, null, "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, null, null, 1231849303, 1116643672, 1102072724, 1253162301, 0, "SRX8003657", "SRS6377637", "SRA1059429", "GEO", "Poss, Cell Biology, Duke University", 1, 0.89702, null, 0.07131, null, 0.82978, null, 0.49499, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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.", null, "pubmed:33408418", null, "high Erk activity; rep2", "GSM4433142", null, "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 \u00b5m 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 \u2013 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 \u00b5l 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 \u00b5l of supernatant was removed  quenched with 65\u00b5l sheep serum Sigma S2263 on ice  and 500 \u00b5l of fresh Liberase was added to the primary tube. All collected supernatant was filtered using 50 \u00b5l filters Corning #431750  pelleted 5 min at 600 g and resuspended in 1 ml DMEM + 1% BSA UltraPure   Invitrogen AM2616.  Before sorting  1 \u00b5g/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", null, "1", "RNA was extracted using TriReagent followed by RNAeasy microKit Qiagen #74004 Library preparation was performed by BGI Genomics Low Input Library Preparation \u2013 BT01", "GEO Accession:GSM4433142", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP254053", null, null, "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, null, null, 1200601624, 1150903127, 1136628277, 1220490572, 0, "SRX8003656", "SRS6377636", "SRA1059429", "GEO", "Poss, Cell Biology, Duke University", 1, 0.90729, null, 0.03751, null, 0.84433, null, 0.50342, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "United States", "2020-03-25", "Undetermined", "Undetermined", "Bone or Cartilage", "Skeletal Element"], [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", null, "Tumor cells  JQ1 day3 rep3 RNA Seq", "GSM5602251", null, "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", null, "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", null, "SRP339154", null, null, "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, null, null, 1214627731, 1045617960, 1070259567, 1221524742, 0, "SRX12388690", "SRS10358692", "SRA1302013", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.93576, null, 0.23142, null, 0.74144, null, 0.48177, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "Tumor cells  JQ1 day3 rep2 RNA Seq", "GSM5602250", null, "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", null, "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", null, "SRP339154", null, null, "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, null, null, 1189464447, 1030660361, 1055524478, 1200265914, 0, "SRX12388689", "SRS10358691", "SRA1302013", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94062, null, 0.18735, null, 0.69759, null, 0.49542, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "Tumor cells  JQ1 day3 rep1 RNA Seq", "GSM5602249", null, "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", null, "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", null, "SRP339154", null, null, "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, null, null, 1179373951, 1024313469, 1050720604, 1187738776, 0, "SRX12388688", "SRS10358690", "SRA1302013", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94195, null, 0.23006, null, 0.72894, null, 0.4972, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "Tumor cells  DMSO day3 rep3 RNA Seq", "GSM5602248", null, "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", null, "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", null, "SRP339154", null, null, "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, null, null, 1202900253, 1006105416, 1022157182, 1215238749, 0, "SRX12388687", "SRS10358689", "SRA1302013", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.95301, null, 0.35614, null, 0.79961, null, 0.50405, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "Tumor cells  DMSO day3 rep2 RNA Seq", "GSM5602247", null, "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", null, "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", null, "SRP339154", null, null, "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, null, null, 1202802143, 1015451294, 1025320457, 1215781706, 0, "SRX12388686", "SRS10358687", "SRA1302013", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.9443, null, 0.32993, null, 0.77786, null, 0.50186, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "Tumor cells  DMSO day3 rep1 RNA Seq", "GSM5602246", null, "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", null, "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", null, "SRP339154", null, null, "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, null, null, 1182551057, 1045032741, 1067880067, 1191207335, 0, "SRX12388685", "SRS10358686", "SRA1302013", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94059, null, 0.21995, null, 0.76658, null, 0.47389, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "Tumor cells  JQ1 day1 rep3 RNA Seq", "GSM5602245", null, "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", null, "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", null, "SRP339154", null, null, "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, null, null, 1213052369, 1047508174, 1069309019, 1220600438, 0, "SRX12388684", "SRS10358685", "SRA1302013", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94051, null, 0.24901, null, 0.74899, null, 0.50515, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "Tumor cells  JQ1 day1 rep2 RNA Seq", "GSM5602244", null, "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", null, "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", null, "SRP339154", null, null, "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, null, null, 1197596235, 1031109315, 1057301946, 1204137304, 0, "SRX12388683", "SRS10358684", "SRA1302013", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94477, null, 0.24522, null, 0.74042, null, 0.51025, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "Tumor cells  JQ1 day1 rep1 RNA Seq", "GSM5602243", null, "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", null, "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", null, "SRP339154", null, null, "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, null, null, 1178050199, 1024865996, 1046777721, 1185193884, 0, "SRX12388682", "SRS10358688", "SRA1302013", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94501, null, 0.2305, null, 0.76432, null, 0.49472, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "Tumor cells  DMSO day1 rep3 RNA Seq", "GSM5602242", null, "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", null, "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", null, "SRP339154", null, null, "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, null, null, 1193693228, 1038160916, 1064460652, 1201568004, 0, "SRX12388681", "SRS10358683", "SRA1302013", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.93714, null, 0.19697, null, 0.74554, null, 0.50928, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "Tumor cells  DMSO day1 rep2 RNA Seq", "GSM5602241", null, "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", null, "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", null, "SRP339154", null, null, "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, null, null, 1185692334, 1031585570, 1050205768, 1196612528, 0, "SRX12388680", "SRS10358682", "SRA1302013", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94785, null, 0.24425, null, 0.78165, null, 0.4975, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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", null, "Tumor cells  DMSO day1 rep1 RNA Seq", "GSM5602240", null, "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", null, "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", null, "SRP339154", null, null, "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, null, null, 1191785539, 1024344626, 1050598581, 1199773454, 0, "SRX12388679", "SRS10358681", "SRA1302013", "GEO", "Takaomi Sanda Lab, Cancer Science Institute, National University of Singapore", 1, 0.94073, null, 0.24308, null, 0.77094, null, 0.48493, null, 100, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Singapore", "2021-09-28", "Undetermined", "Undetermined", "Cancer or Tumor", "Cancer or Tumor"], [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\u2013PCR.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.", null, "pubmed:38242380", null, "testes", "GSM7099751", null, "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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP427394", null, null, "WT-testis.fq.gz", "fastq", 1176068400.0, 23521368.0, "GSM7099751 r1", "0:50", "A:323799672;C:262049848;G:273563529;T:316045968;N:609383", 50, null, null, null, 323799672, 262049848, 273563529, 316045968, 609383, "SRX19680348", "SRS17049789", "SRA1687194", "Wuhan university", "Wuhan university", 1, 0.93023, null, 0.11308, null, 0.6462, null, 0.49784, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "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\u2013PCR.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.", null, "pubmed:38242380", null, "ovaries", "GSM7099752", null, "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", null, "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.", null, "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.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP427394", null, null, "WT-ovary.fq.gz", "fastq", 1176463600.0, 23529272.0, "GSM7099752 r1", "0:50", "A:311869864;C:270650722;G:289863261;T:303489229;N:590524", 50, null, null, null, 311869864, 270650722, 289863261, 303489229, 590524, "SRX19680347", "SRS17049788", "SRA1687194", "Wuhan university", "Wuhan university", 1, 0.93488, null, 0.02755, null, 0.75601, null, 0.46986, null, 50, null, "B", null, "usable mapping rate", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2023-03-15", "Undetermined", "Undetermined", "Gonad", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 32, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", 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earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation_coarse\" = :p0 and \"experiment.platform\" = :p1 order by rowid limit 101", "params": {"p0": "Undetermined", "p1": "BGISEQ"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 32, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ&experiment.library_strategy=RNA-Seq", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 32, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ", "results": [{"value": "cDNA", "label": "cDNA", "count": 32, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ", "results": [{"value": "BGISEQ", "label": "BGISEQ", "count": 32, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined", "selected": true}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 32, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.platform=BGISEQ", "selected": true}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ", "results": [{"value": "Undetermined", "label": "Undetermined", "count": 32, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ&devstage_curation=Undetermined", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ", "results": [{"value": "Cancer or Tumor", "label": "Cancer or Tumor", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ&tissue_curation_coarse=Cancer+or+Tumor", "selected": false}, {"value": "Multi-system", "label": "Multi-system", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ&tissue_curation_coarse=Multi-system", "selected": false}, {"value": "Skeletal Element", "label": "Skeletal 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"Cancer or Tumor", "label": "Cancer or Tumor", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ&tissue_curation=Cancer+or+Tumor", "selected": false}, {"value": "Bone or Cartilage", "label": "Bone or Cartilage", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ&tissue_curation=Bone+or+Cartilage", "selected": false}, {"value": "Multi-tissue", "label": "Multi-tissue", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Undetermined&experiment.platform=BGISEQ&tissue_curation=Multi-tissue", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 6, "toggle_url": 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