run_metadata
138 rows where experiment.platform = "BGISEQ" and tissue_curation_coarse = "Undetermined"
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| Link | rowid ▼ | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 28794 | 28794 | SRR26685983 | SRX22385777 | SRS19431939 | SRP470412 | PRJNA1036238 | RNAseq of Wild Type and pikfyve?8 zebrafish. | GSE247110 | Transcriptome Analysis | Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish. | pikfyve3 | GSM7883488 | source name:genotype|tissue:genotype|genotype:pikfyve delta8|geo loc name:missing|collection date:missing | pikfyve3 | Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample | genotype | The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing | tissue:genotype|genotype:pikfyve delta8 | GSM7883488 | GSM7883488: pikfyve3; Danio rerio; RNA Seq | GSM7883488 r1 | GSM7883488 | 1 | The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP470412 | pikfyve3_1.fq.gz pikfyve3_2.fq.gz | fastq fastq | 6618846900.0 | 22062823.0 | GSM7883488 r1 | 0:150 1:150 | A:1763884594;C:1537497822;G:1533232898;T:1784136042;N:95544 | 150 | 150 | 1763884594 | 1537497822 | 1533232898 | 1784136042 | 95544 | SRX22385777 | SRS19431939 | SRA1746433 | The Second Clinical Medical College, Jinan University | The Second Clinical Medical College, Jinan University | 2 | 0.93396 | 0.92718 | 0.09419 | 0.09305 | 0.66348 | 0.66496 | 0.48704 | 0.4839 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-11-06 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||
| 28795 | 28795 | SRR26685984 | SRX22385776 | SRS19431938 | SRP470412 | PRJNA1036238 | RNAseq of Wild Type and pikfyve?8 zebrafish. | GSE247110 | Transcriptome Analysis | Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish. | pikfyve2 | GSM7883487 | source name:genotype|tissue:genotype|genotype:pikfyve delta8|geo loc name:missing|collection date:missing | pikfyve2 | Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample | genotype | The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing | tissue:genotype|genotype:pikfyve delta8 | GSM7883487 | GSM7883487: pikfyve2; Danio rerio; RNA Seq | GSM7883487 r1 | GSM7883487 | 1 | The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP470412 | pikfyve2_1.fq.gz pikfyve2_2.fq.gz | fastq fastq | 6640406100.0 | 22134687.0 | GSM7883487 r1 | 0:150 1:150 | A:1765647548;C:1547424271;G:1541609810;T:1785639698;N:84773 | 150 | 150 | 1765647548 | 1547424271 | 1541609810 | 1785639698 | 84773 | SRX22385776 | SRS19431938 | SRA1746433 | The Second Clinical Medical College, Jinan University | The Second Clinical Medical College, Jinan University | 2 | 0.93535 | 0.92946 | 0.08654 | 0.08582 | 0.67127 | 0.67298 | 0.48517 | 0.48183 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-11-06 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||
| 28796 | 28796 | SRR26685985 | SRX22385775 | SRS19431937 | SRP470412 | PRJNA1036238 | RNAseq of Wild Type and pikfyve?8 zebrafish. | GSE247110 | Transcriptome Analysis | Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish. | pikfyve1 | GSM7883486 | source name:genotype|tissue:genotype|genotype:pikfyve delta8|geo loc name:missing|collection date:missing | pikfyve1 | Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample | genotype | The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing | tissue:genotype|genotype:pikfyve delta8 | GSM7883486 | GSM7883486: pikfyve1; Danio rerio; RNA Seq | GSM7883486 r1 | GSM7883486 | 1 | The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP470412 | pikfyve1_1.fq.gz pikfyve1_2.fq.gz | fastq fastq | 6629613600.0 | 22098712.0 | GSM7883486 r1 | 0:150 1:150 | A:1765377736;C:1543131511;G:1535515864;T:1785505926;N:82563 | 150 | 150 | 1765377736 | 1543131511 | 1535515864 | 1785505926 | 82563 | SRX22385775 | SRS19431937 | SRA1746433 | The Second Clinical Medical College, Jinan University | The Second Clinical Medical College, Jinan University | 2 | 0.93638 | 0.92994 | 0.08782 | 0.08654 | 0.67138 | 0.67119 | 0.47859 | 0.47753 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-11-06 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||
| 28797 | 28797 | SRR26685986 | SRX22385774 | SRS19431936 | SRP470412 | PRJNA1036238 | RNAseq of Wild Type and pikfyve?8 zebrafish. | GSE247110 | Transcriptome Analysis | Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish. | WT3 | GSM7883485 | source name:genotype|tissue:genotype|genotype:Wile Type|geo loc name:missing|collection date:missing | WT3 | Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample | genotype | The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing | tissue:genotype|genotype:Wile Type | GSM7883485 | GSM7883485: WT3; Danio rerio; RNA Seq | GSM7883485 r1 | GSM7883485 | 1 | The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP470412 | WT3_2.fq.gz WT3_1.fq.gz | fastq fastq | 6654357000.0 | 22181190.0 | GSM7883485 r1 | 0:150 1:150 | A:1778694761;C:1540249434;G:1534346559;T:1801052542;N:13704 | 150 | 150 | 1778694761 | 1540249434 | 1534346559 | 1801052542 | 13704 | SRX22385774 | SRS19431936 | SRA1746433 | The Second Clinical Medical College, Jinan University | The Second Clinical Medical College, Jinan University | 2 | 0.93688 | 0.92644 | 0.09182 | 0.09071 | 0.66229 | 0.66434 | 0.48313 | 0.48263 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-11-06 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||
| 28798 | 28798 | SRR26685987 | SRX22385773 | SRS19431935 | SRP470412 | PRJNA1036238 | RNAseq of Wild Type and pikfyve?8 zebrafish. | GSE247110 | Transcriptome Analysis | Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish. | WT2 | GSM7883484 | source name:genotype|tissue:genotype|genotype:Wile Type|geo loc name:missing|collection date:missing | WT2 | Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample | genotype | The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing | tissue:genotype|genotype:Wile Type | GSM7883484 | GSM7883484: WT2; Danio rerio; RNA Seq | GSM7883484 r1 | GSM7883484 | 1 | The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP470412 | WT2_1.fq.gz WT2_2.fq.gz | fastq fastq | 6661129500.0 | 22203765.0 | GSM7883484 r1 | 0:150 1:150 | A:1774160269;C:1545605554;G:1545211257;T:1796139014;N:13406 | 150 | 150 | 1774160269 | 1545605554 | 1545211257 | 1796139014 | 13406 | SRX22385773 | SRS19431935 | SRA1746433 | The Second Clinical Medical College, Jinan University | The Second Clinical Medical College, Jinan University | 2 | 0.93696 | 0.9278 | 0.08665 | 0.08477 | 0.66322 | 0.66498 | 0.48376 | 0.48557 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-11-06 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||
| 28799 | 28799 | SRR26685988 | SRX22385772 | SRS19431934 | SRP470412 | PRJNA1036238 | RNAseq of Wild Type and pikfyve?8 zebrafish. | GSE247110 | Transcriptome Analysis | Purpose: Phosphoinositide kinase FYVE type zinc finger containing PIKFYVE is a newly identified pathogenic gene involved in cataract. This study aimed to investigate the nature and mechanism of vacuoles related to PIKFYVE. Methods: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. The pikfyve?8 homozygous and wild type zebrafish were subjected to transcriptomic analyses. Results: Transcriptomic analyses revealed 8694 differentially expressed genes DEGs. Conclusion: Our study represents the first detalis transcriptomic analysis of pikfyve disruption zebrafish. Overall design: We generated Pikfyve phosphatidylinositol phosphate kinase domain deficient pikfyve?8 zebrafish using CRISPR/Cas9 directed gene editing. We then performed gene expression profiling analysis using data obtained from RNAseq of three samples respectively in pikfyve?8 homozygous and wild type zebrafish. | WT1 | GSM7883483 | source name:genotype|tissue:genotype|genotype:Wile Type|geo loc name:missing|collection date:missing | WT1 | Data filtering The sequencing data was filtered with SOAPnuke [1] by 1 Removing reads containing sequencing adapter; 2 Removing reads whose low quality base ratio base quality less than or equal to 15 is more than 20%; 3 Removing reads whose unknown base 'N' base ratio is more than 5% postwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi omics Data mining system https://biosys.bgi.com. RNA identification Bowtie2[2] was applied to align the clean reads to the gene set in which known and novel coding and noncoding transcripts were included. Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM v1.3.1 [3]. The heatmap was drawn by pheatmap v1.0.8 [4] according to the gene expression difference in different samples. Essentially differential expression analysis was performed using the DESeq2v1.4.5 [5] or DEGseq[6] or PoissonDis[7]with Q value ≤ 0.05 or FDR ≤ 0.001. Gene Annotation To take insight to the change of phenotype GO http://www.geneontology.org/ and KEGG https://www.kegg.jp/ enrichment analysis of annotated different expression gene was performed by Phyper https://en.wikipedia.org/wiki/Hypergeometric distribution based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold Q value ≤ 0.05 [8]. Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: text file includes raw counts for each Sample Supplementary files format and content: text files include RPKM values for each Sample | genotype | The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing | tissue:genotype|genotype:Wile Type | GSM7883483 | GSM7883483: WT1; Danio rerio; RNA Seq | GSM7883483 r1 | GSM7883483 | 1 | The sample RNA was extracted and purified using the Qiagen kit 1Select the corresponding testing methods for quality inspection according to the requirements of samples and products. 2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single stranded cyclized products are produced while uncyclized linear DNA molecules are digested. 9 Sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP470412 | WT1_2.fq.gz WT1_1.fq.gz | fastq fastq | 6648386700.0 | 22161289.0 | GSM7883483 r1 | 0:150 1:150 | A:1780975057;C:1536473791;G:1530388485;T:1800462718;N:86649 | 150 | 150 | 1780975057 | 1536473791 | 1530388485 | 1800462718 | 86649 | SRX22385772 | SRS19431934 | SRA1746433 | The Second Clinical Medical College, Jinan University | The Second Clinical Medical College, Jinan University | 2 | 0.93595 | 0.92974 | 0.09487 | 0.09314 | 0.65969 | 0.66005 | 0.48731 | 0.4845 | 150 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2023-11-06 | Undetermined | Undetermined | Undetermined | Undetermined | |||||||||||||
| 31825 | 31825 | SRR28700412 | SRX24268115 | SRS21034395 | SRP501894 | PRJNA1100624 | Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis | PRJNA1100624 | Other | Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP. | PN 2 | isolate:PN2|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal | RNA Seq of zebrafish | PN 2 | PN 2 | Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP501894 | PN_2_1.fq.gz PN_2_2.fq.gz | fastq fastq | 6385048200.0 | 21283494.0 | PN 2 1.fq.gz | 0:150 1:150 | A:1722127999;C:1463645587;G:1483173818;T:1716100796;N:0 | 150 | 150 | 1722127999 | 1463645587 | 1483173818 | 1716100796 | 0 | SRX24268115 | SRS21034395 | Xiangyang No.1 People's Hospital, Hubei University of Medicine | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-04-15 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||||||||||||||||||
| 31826 | 31826 | SRR28700413 | SRX24268114 | SRS21034397 | SRP501894 | PRJNA1100624 | Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis | PRJNA1100624 | Other | Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP. | PN 1 | isolate:PN1|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal | RNA Seq of zebrafish | PN 1 | PN 1 | Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP501894 | PN_1_1.fq.gz PN_1_2.fq.gz | fastq fastq | 6692894100.0 | 22309647.0 | PN 1 1.fq.gz | 0:150 1:150 | A:1827107021;C:1513034624;G:1533077624;T:1819674831;N:0 | 150 | 150 | 1827107021 | 1513034624 | 1533077624 | 1819674831 | 0 | SRX24268114 | SRS21034397 | Xiangyang No.1 People's Hospital, Hubei University of Medicine | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-04-15 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||||||||||||||||||
| 31827 | 31827 | SRR28700414 | SRX24268113 | SRS21034396 | SRP501894 | PRJNA1100624 | Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis | PRJNA1100624 | Other | Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP. | EC 4 | isolate:EC4|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal | RNA Seq of zebrafish | EC 4 | EC 4 | Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP501894 | EC_4_1.fq.gz EC_4_2.fq.gz | fastq fastq | 6688857000.0 | 22296190.0 | EC 4 1.fq.gz | 0:150 1:150 | A:1820989545;C:1516814697;G:1537970654;T:1813082104;N:0 | 150 | 150 | 1820989545 | 1516814697 | 1537970654 | 1813082104 | 0 | SRX24268113 | SRS21034396 | Xiangyang No.1 People's Hospital, Hubei University of Medicine | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-04-15 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||||||||||||||||||
| 31828 | 31828 | SRR28700415 | SRX24268112 | SRS21034392 | SRP501894 | PRJNA1100624 | Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis | PRJNA1100624 | Other | Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP. | EC 3 | isolate:EC3|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal | RNA Seq of zebrafish | EC 3 | EC 3 | Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP501894 | EC_3_1.fq.gz EC_3_2.fq.gz | fastq fastq | 6696553800.0 | 22321846.0 | EC 3 1.fq.gz | 0:150 1:150 | A:1821249100;C:1520587242;G:1541238550;T:1813478908;N:0 | 150 | 150 | 1821249100 | 1520587242 | 1541238550 | 1813478908 | 0 | SRX24268112 | SRS21034392 | Xiangyang No.1 People's Hospital, Hubei University of Medicine | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-04-15 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||||||||||||||||||
| 31829 | 31829 | SRR28700416 | SRX24268111 | SRS21034391 | SRP501894 | PRJNA1100624 | Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis | PRJNA1100624 | Other | Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP. | EC 2 | isolate:EC2|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal | RNA Seq of zebrafish | EC 2 | EC 2 | Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP501894 | EC_2_1.fq.gz EC_2_2.fq.gz | fastq fastq | 6702179400.0 | 22340598.0 | EC 2 1.fq.gz | 0:150 1:150 | A:1816692261;C:1527379142;G:1547365810;T:1810742187;N:0 | 150 | 150 | 1816692261 | 1527379142 | 1547365810 | 1810742187 | 0 | SRX24268111 | SRS21034391 | Xiangyang No.1 People's Hospital, Hubei University of Medicine | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-04-15 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||||||||||||||||||
| 31830 | 31830 | SRR28700417 | SRX24268110 | SRS21034390 | SRP501894 | PRJNA1100624 | Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis | PRJNA1100624 | Other | Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP. | EC 1 | isolate:EC1|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal | RNA Seq of zebrafish | EC 1 | EC 1 | Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP501894 | EC_1_1.fq.gz EC_1_2.fq.gz | fastq fastq | 6686053500.0 | 22286845.0 | EC 1 1.fq.gz | 0:150 1:150 | A:1812022780;C:1524359858;G:1544847441;T:1804823421;N:0 | 150 | 150 | 1812022780 | 1524359858 | 1544847441 | 1804823421 | 0 | SRX24268110 | SRS21034390 | Xiangyang No.1 People's Hospital, Hubei University of Medicine | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-04-15 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||||||||||||||||||
| 31831 | 31831 | SRR28700418 | SRX24268109 | SRS21034388 | SRP501894 | PRJNA1100624 | Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis | PRJNA1100624 | Other | Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP. | Control 4 | isolate:con4|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal | RNA Seq of zebrafish | Control 4 | Control 4 | Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP501894 | Control_4_1.fq.gz Control_4_2.fq.gz | fastq fastq | 6669700500.0 | 22232335.0 | Control 4 1.fq.gz | 0:150 1:150 | A:1804178265;C:1523547469;G:1543839484;T:1798135282;N:0 | 150 | 150 | 1804178265 | 1523547469 | 1543839484 | 1798135282 | 0 | SRX24268109 | SRS21034388 | Xiangyang No.1 People's Hospital, Hubei University of Medicine | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-04-15 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||||||||||||||||||
| 31832 | 31832 | SRR28700419 | SRX24268108 | SRS21034387 | SRP501894 | PRJNA1100624 | Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis | PRJNA1100624 | Other | Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP. | Control 3 | isolate:con3|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal | RNA Seq of zebrafish | Control 3 | Control 3 | Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP501894 | Control_3_1.fq.gz Control_3_2.fq.gz | fastq fastq | 6683518800.0 | 22278396.0 | Control 3 1.fq.gz | 0:150 1:150 | A:1808495506;C:1525725204;G:1545930043;T:1803368047;N:0 | 150 | 150 | 1808495506 | 1525725204 | 1545930043 | 1803368047 | 0 | SRX24268108 | SRS21034387 | Xiangyang No.1 People's Hospital, Hubei University of Medicine | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-04-15 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||||||||||||||||||
| 31833 | 31833 | SRR28700420 | SRX24268107 | SRS21034386 | SRP501894 | PRJNA1100624 | Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis | PRJNA1100624 | Other | Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP. | PN 4 | isolate:PN4|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 4|BioSampleModel:Model organism or animal | RNA Seq of zebrafish | PN 4 | PN 4 | Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP501894 | PN_4_1.fq.gz PN_4_2.fq.gz | fastq fastq | 6649316100.0 | 22164387.0 | PN 4 1.fq.gz | 0:150 1:150 | A:1809816121;C:1508072480;G:1528272654;T:1803154845;N:0 | 150 | 150 | 1809816121 | 1508072480 | 1528272654 | 1803154845 | 0 | SRX24268107 | SRS21034386 | Xiangyang No.1 People's Hospital, Hubei University of Medicine | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-04-15 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||||||||||||||||||
| 31834 | 31834 | SRR28700421 | SRX24268106 | SRS21034389 | SRP501894 | PRJNA1100624 | Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis | PRJNA1100624 | Other | Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP. | PN 3 | isolate:PN3|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 3|BioSampleModel:Model organism or animal | RNA Seq of zebrafish | PN 3 | PN 3 | Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP501894 | PN_3_1.fq.gz PN_3_2.fq.gz | fastq fastq | 6616113900.0 | 22053713.0 | PN 3 1.fq.gz | 0:150 1:150 | A:1802283686;C:1499008018;G:1519150002;T:1795672194;N:0 | 150 | 150 | 1802283686 | 1499008018 | 1519150002 | 1795672194 | 0 | SRX24268106 | SRS21034389 | Xiangyang No.1 People's Hospital, Hubei University of Medicine | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-04-15 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||||||||||||||||||
| 31835 | 31835 | SRR28700422 | SRX24268105 | SRS21034385 | SRP501894 | PRJNA1100624 | Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis | PRJNA1100624 | Other | Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP. | Control 2 | isolate:con2|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 2|BioSampleModel:Model organism or animal | RNA Seq of zebrafish | Control 2 | Control 2 | Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP501894 | Control_2_1.fq.gz Control_2_2.fq.gz | fastq fastq | 6701719200.0 | 22339064.0 | Control 2 1.fq.gz | 0:150 1:150 | A:1812352260;C:1531672703;G:1551377072;T:1806317165;N:0 | 150 | 150 | 1812352260 | 1531672703 | 1551377072 | 1806317165 | 0 | SRX24268105 | SRS21034385 | Xiangyang No.1 People's Hospital, Hubei University of Medicine | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-04-15 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||||||||||||||||||
| 31836 | 31836 | SRR28700423 | SRX24268104 | SRS21034384 | SRP501894 | PRJNA1100624 | Functions of Epimedin C in a zebrafish model of glucocorticoid induced osteoporosis | PRJNA1100624 | Other | Research indicates that Epimedin C EC an active compound in Epimedium offers a potential treatment for glucocorticoid induced osteoporosis GIOP. Studies on zebrafish larvae revealed that EC treatment enhances bone mineralization increases bone mass and improves bone density thus mitigating bone tissue damage caused by prednisolone. Additionally EC impacts key signaling pathways related to bone development such as osteoclast differentiation estrogen MAPK insulin resistance PPAR and AMPK pathways. This study highlights EC's role in bone health and its promising osteoprotective effects presenting it as a viable cost effective treatment for GIOP. | Control 1 | isolate:con1|age:9dpf|collection date:2023 07 13|geo loc name:China:Hubei Xiangyang|sex:not collected|tissue:animal sample|replicate:replicate = biological replicate 1|BioSampleModel:Model organism or animal | RNA Seq of zebrafish | Control 1 | Control 1 | Total RNA undergoes mRNA enrichment reverse transcription adapter ligation PCR amplification and circularization into a single stranded DNA library. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP501894 | Control_1_1.fq.gz Control_1_2.fq.gz | fastq fastq | 6720214500.0 | 22400715.0 | Control 1 1.fq.gz | 0:150 1:150 | A:1814883015;C:1537948710;G:1559376116;T:1808006659;N:0 | 150 | 150 | 1814883015 | 1537948710 | 1559376116 | 1808006659 | 0 | SRX24268104 | SRS21034384 | Xiangyang No.1 People's Hospital, Hubei University of Medicine | B | B | biological fallback assumption | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2024-04-15 | Larval | Larval | Undetermined | Undetermined | ||||||||||||||||||||||||||||||||||
| 52210 | 52210 | SRR9021058 | SRX5799154 | SRS4730324 | SRP195685 | PRJNA541367 | Global transcriptomic analysis of zebrafish glucagon receptor mutant | PRJNA541367 | Other | We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study. | WT 1 | replicate:biological replicate 1|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal | Diano rerio transcriptome | WT 1 20190506 1 | WT 1 20190506 1 | RNA seq of WT Diano rerio | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | BGISEQ | BGISEQ-500 | SRP195685 | loader:fastq load.py | WT1.1.fq | fastq | 1094498950.0 | 21889979.0 | WT1.1.fq | 0:50 | A:291195764;C:255539280;G:262638316;T:284737693;N:387897 | 50 | 291195764 | 255539280 | 262638316 | 284737693 | 387897 | SRX5799154 | SRS4730324 | SRA883435 | Xiamen University|School of Pharmaceutical Sciences | Xiamen University | 1 | 0.94195 | 0.09713 | 0.66689 | 0.47749 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2020-01-18 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 52211 | 52211 | SRR9021059 | SRX5799153 | SRS4730323 | SRP195685 | PRJNA541367 | Global transcriptomic analysis of zebrafish glucagon receptor mutant | PRJNA541367 | Other | We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study. | WT 2 | replicate:biological replicate 2|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal | Diano rerio transcriptome | WT 2 20190506 2 | WT 2 20190506 2 | RNA seq of WT Diano rerio | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | BGISEQ | BGISEQ-500 | SRP195685 | loader:fastq load.py | WT2.1.fq | fastq | 1095133200.0 | 21902664.0 | WT2.1.fq | 0:50 | A:290594757;C:255644044;G:259681140;T:288014102;N:1199157 | 50 | 290594757 | 255644044 | 259681140 | 288014102 | 1199157 | SRX5799153 | SRS4730323 | SRA883435 | Xiamen University|School of Pharmaceutical Sciences | Xiamen University | 1 | 0.93368 | 0.09166 | 0.67085 | 0.46523 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2020-01-18 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 52212 | 52212 | SRR9021060 | SRX5799152 | SRS4730322 | SRP195685 | PRJNA541367 | Global transcriptomic analysis of zebrafish glucagon receptor mutant | PRJNA541367 | Other | We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study. | WT 3 | replicate:biological replicate 3|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal | Diano rerio transcriptome | WT 3 20190506 3 | WT 3 20190506 3 | RNA seq of WT Diano rerio | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | BGISEQ | BGISEQ-500 | SRP195685 | loader:fastq load.py | WT3.1.fq | fastq | 1096083900.0 | 21921678.0 | WT3.1.fq | 0:50 | A:290332094;C:256993500;G:263043956;T:285349722;N:364628 | 50 | 290332094 | 256993500 | 263043956 | 285349722 | 364628 | SRX5799152 | SRS4730322 | SRA883435 | Xiamen University|School of Pharmaceutical Sciences | Xiamen University | 1 | 0.94147 | 0.10157 | 0.66135 | 0.47301 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2020-01-18 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 52213 | 52213 | SRR9021061 | SRX5799151 | SRS4730320 | SRP195685 | PRJNA541367 | Global transcriptomic analysis of zebrafish glucagon receptor mutant | PRJNA541367 | Other | We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study. | gcgr 1 | replicate:biological replicate 1|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal | Diano rerio transcriptome | gcgr 1 20190506 1 | gcgr 1 20190506 1 | RNA seq of Diano rerio with gcgr mutant | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | BGISEQ | BGISEQ-500 | SRP195685 | loader:fastq load.py | gcgr1.1.fq | fastq | 1096307200.0 | 21926144.0 | gcgr1.1.fq | 0:50 | A:288839446;C:258297625;G:264630675;T:284199738;N:339716 | 50 | 288839446 | 258297625 | 264630675 | 284199738 | 339716 | SRX5799151 | SRS4730320 | SRA883435 | Xiamen University|School of Pharmaceutical Sciences | Xiamen University | 1 | 0.94131 | 0.09307 | 0.67574 | 0.46993 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2020-01-18 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 52214 | 52214 | SRR9021062 | SRX5799150 | SRS4730321 | SRP195685 | PRJNA541367 | Global transcriptomic analysis of zebrafish glucagon receptor mutant | PRJNA541367 | Other | We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study. | gcgr 2 | replicate:biological replicate 2|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal | Diano rerio transcriptome | gcgr 2 20190506 2 | gcgr 2 20190506 2 | RNA seq of Diano rerio with gcgr mutant | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | BGISEQ | BGISEQ-500 | SRP195685 | loader:fastq load.py | gcgr2.1.fq | fastq | 1094410100.0 | 21888202.0 | gcgr2.1.fq | 0:50 | A:290062779;C:256358687;G:264488431;T:282812212;N:687991 | 50 | 290062779 | 256358687 | 264488431 | 282812212 | 687991 | SRX5799150 | SRS4730321 | SRA883435 | Xiamen University|School of Pharmaceutical Sciences | Xiamen University | 1 | 0.94074 | 0.09337 | 0.67633 | 0.46861 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2020-01-18 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 52215 | 52215 | SRR9021063 | SRX5799149 | SRS4730319 | SRP195685 | PRJNA541367 | Global transcriptomic analysis of zebrafish glucagon receptor mutant | PRJNA541367 | Other | We performed RNA sequencing RNA seq analysis of whole fish to provide a comprehensive view of its global transcriptomic regulation in this study. | gcgr 3 | replicate:biological replicate 3|strain:AB|age:7 days|sex:not applicable|tissue:total|BioSampleModel:Model organism or animal | Diano rerio transcriptome | gcgr 3 20190506 3 | gcgr 3 20190506 3 | RNA seq of Diano rerio with gcgr mutant | RNA-Seq | TRANSCRIPTOMIC | other | SINGLE | BGISEQ | BGISEQ-500 | SRP195685 | loader:fastq load.py | gcgr3.1.fq | fastq | 1094284800.0 | 21885696.0 | gcgr3.1.fq | 0:50 | A:289313514;C:257096636;G:264011408;T:283143600;N:719642 | 50 | 289313514 | 257096636 | 264011408 | 283143600 | 719642 | SRX5799149 | SRS4730319 | SRA883435 | Xiamen University|School of Pharmaceutical Sciences | Xiamen University | 1 | 0.94222 | 0.09557 | 0.67521 | 0.46664 | 50 | B | usable mapping rate | bgi | bgi | unknown | random_priming | unknown | bulk | unknown | unknown | China | 2020-01-18 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 55643 | 55643 | SRR10604044 | SRX7283593 | SRS5777402 | SRP235014 | PRJNA594101 | Danio rerio Transcriptome | PRJNA594101 | Other | Danio rerio Transcriptome post cGAS and STING knockout | stko2 | strain:not collected|isolate:sting knockout 2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:7 days|dev stage:larvae|sex:not applicable|tissue:larvae|biomaterial provider:Yang xiaojun|BioSampleModel:Model organism or animal | RNA Seq of zebraish larvae | sting knockout 2 | sting knockout 2 | RNA seq | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP235014 | stko2_1.fastq.gz stko2_2.fastq.gz | fastq fastq | 10635609300.0 | 70904062.0 | stko2 1.fastq.gz | 0:150 1:150 | A:2864931942;C:2450585568;G:2436540783;T:2882828480;N:722527 | 150 | 150 | 2864931942 | 2450585568 | 2436540783 | 2882828480 | 722527 | SRX7283593 | SRS5777402 | SRA1007465 | Shantou university medical college|Neuroscience Center | Shantou university medical college | 1 | 0.93079 | 0.07849 | 0.70301 | 0.47872 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2019-12-08 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 55644 | 55644 | SRR10604045 | SRX7283592 | SRS5777401 | SRP235014 | PRJNA594101 | Danio rerio Transcriptome | PRJNA594101 | Other | Danio rerio Transcriptome post cGAS and STING knockout | stko1 | strain:not collected|isolate:sting knockout 1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:7 days|dev stage:larvae|sex:not applicable|tissue:larvae|biomaterial provider:Yang xiaojun|BioSampleModel:Model organism or animal | RNA Seq of zebraish larvae | sting knockout 1 | sting knockout 1 | RNA seq | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP235014 | stko1_1.fastq.gz stko1_2.fastq.gz | fastq fastq | 10453959000.0 | 69693060.0 | stko1 1.fastq.gz | 0:150 1:150 | A:2823253748;C:2400078679;G:2379662427;T:2850274552;N:689594 | 150 | 150 | 2823253748 | 2400078679 | 2379662427 | 2850274552 | 689594 | SRX7283592 | SRS5777401 | SRA1007465 | Shantou university medical college|Neuroscience Center | Shantou university medical college | 1 | 0.92736 | 0.08475 | 0.69822 | 0.47233 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2019-12-08 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 55645 | 55645 | SRR10604046 | SRX7283591 | SRS5777400 | SRP235014 | PRJNA594101 | Danio rerio Transcriptome | PRJNA594101 | Other | Danio rerio Transcriptome post cGAS and STING knockout | cgko2 | strain:not collected|isolate:cgas knockout 2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:7 days|dev stage:larvae|sex:not applicable|tissue:larvae|biomaterial provider:Yang xiaojun|BioSampleModel:Model organism or animal | RNA Seq of zebraish larvae | cgas knockout 2 | cgas knockout 2 | RNA seq | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP235014 | cgko2_1.fastq.gz cgko2_2.fastq.gz | fastq fastq | 10462236900.0 | 69748246.0 | cgko2 1.fastq.gz | 0:150 1:150 | A:2836737922;C:2388112649;G:2370425883;T:2866326601;N:633845 | 150 | 150 | 2836737922 | 2388112649 | 2370425883 | 2866326601 | 633845 | SRX7283591 | SRS5777400 | SRA1007465 | Shantou university medical college|Neuroscience Center | Shantou university medical college | 1 | 0.93603 | 0.10606 | 0.67765 | 0.46153 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2019-12-08 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 55646 | 55646 | SRR10604047 | SRX7283590 | SRS5777399 | SRP235014 | PRJNA594101 | Danio rerio Transcriptome | PRJNA594101 | Other | Danio rerio Transcriptome post cGAS and STING knockout | cgko1 | strain:not collected|isolate:cgas knockout 1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:7 days|dev stage:larvae|sex:not applicable|tissue:larvae|biomaterial provider:Yang xiaojun|BioSampleModel:Model organism or animal | RNA Seq of zebraish larvae | cgas knockout 1 | cgas knockout 1 | RNA seq | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP235014 | cgko1_2.fastq.gz cgko1_1.fastq.gz | fastq fastq | 10498495500.0 | 69989970.0 | cgko1 1.fastq.gz | 0:150 1:150 | A:2845684832;C:2398817161;G:2379300746;T:2874108573;N:584188 | 150 | 150 | 2845684832 | 2398817161 | 2379300746 | 2874108573 | 584188 | SRX7283590 | SRS5777399 | SRA1007465 | Shantou university medical college|Neuroscience Center | Shantou university medical college | 1 | 0.93684 | 0.10589 | 0.67933 | 0.48363 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2019-12-08 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 55647 | 55647 | SRR10604048 | SRX7283589 | SRS5777398 | SRP235014 | PRJNA594101 | Danio rerio Transcriptome | PRJNA594101 | Other | Danio rerio Transcriptome post cGAS and STING knockout | wt2 | strain:not collected|isolate:normal 2|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:7 days|dev stage:larvae|sex:not applicable|tissue:larvae|biomaterial provider:Yang xiaojun|BioSampleModel:Model organism or animal | RNA Seq of zebraish larvae | wt normal 2 | wt normal 2 | RNA seq | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP235014 | wt2_1.fastq.gz wt2_2.fastq.gz | fastq fastq | 10660916400.0 | 71072776.0 | wt2 1.fastq.gz | 0:150 1:150 | A:2906473511;C:2417423798;G:2405111864;T:2931146507;N:760720 | 150 | 150 | 2906473511 | 2417423798 | 2405111864 | 2931146507 | 760720 | SRX7283589 | SRS5777398 | SRA1007465 | Shantou university medical college|Neuroscience Center | Shantou university medical college | 1 | 0.94167 | 0.11781 | 0.66831 | 0.4757 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2019-12-08 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 55648 | 55648 | SRR10604049 | SRX7283588 | SRS5777397 | SRP235014 | PRJNA594101 | Danio rerio Transcriptome | PRJNA594101 | Other | Danio rerio Transcriptome post cGAS and STING knockout | wt1 | strain:not collected|isolate:normal 1|breed:not applicable|cultivar:not applicable|ecotype:not applicable|age:7 days|dev stage:larvae|sex:not applicable|tissue:larvae|biomaterial provider:Yang xiaojun|BioSampleModel:Model organism or animal | RNA Seq of zebraish larvae | wt nomal 1 | wt nomal 1 | RNA seq | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP235014 | wt1_1.fastq.gz wt1_2.fastq.gz | fastq fastq | 10599804000.0 | 70665360.0 | wt1 1.fastq.gz | 0:150 1:150 | A:2896989124;C:2397285811;G:2382705623;T:2922067937;N:755505 | 150 | 150 | 2896989124 | 2397285811 | 2382705623 | 2922067937 | 755505 | SRX7283588 | SRS5777397 | SRA1007465 | Shantou university medical college|Neuroscience Center | Shantou university medical college | 1 | 0.93947 | 0.11723 | 0.67203 | 0.45826 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2019-12-08 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61375 | 61375 | SRR12687500 | SRX9167472 | SRS7406198 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | AlCl3 1 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:10|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | AlCl3 1 | AlCl3 1 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | AlCl3_1_1.fq AlCl3_1_2.fq | fastq fastq | 6318129000.0 | 63181290.0 | AlCl3 1 1.fq | 0:100 1:100 | A:1703650974;C:1436858038;G:1474640143;T:1702979845;N:0 | 100 | 100 | 1703650974 | 1436858038 | 1474640143 | 1702979845 | 0 | SRX9167472 | SRS7406198 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.92336 | 0.1173 | 0.6981 | 0.47069 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61376 | 61376 | SRR12687501 | SRX9167471 | SRS7406199 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | S3 3 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:9|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | S3 3 | S3 3 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | S3_3_1.fq S3_3_2.fq | fastq fastq | 6896170000.0 | 68961700.0 | S3 3 1.fq | 0:100 1:100 | A:1952511528;C:1476189599;G:1495880823;T:1971588050;N:0 | 100 | 100 | 1952511528 | 1476189599 | 1495880823 | 1971588050 | 0 | SRX9167471 | SRS7406199 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.93819 | 0.18403 | 0.69881 | 0.51999 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61377 | 61377 | SRR12687502 | SRX9167470 | SRS7406197 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | S3 2 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:8|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | S3 2 | S3 2 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | S3_2_1.fq S3_2_2.fq | fastq fastq | 7144137200.0 | 71441372.0 | S3 2 1.fq | 0:100 1:100 | A:2053632992;C:1499315470;G:1512455113;T:2078733625;N:0 | 100 | 100 | 2053632992 | 1499315470 | 1512455113 | 2078733625 | 0 | SRX9167470 | SRS7406197 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.93285 | 0.2066 | 0.70997 | 0.52936 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61378 | 61378 | SRR12687503 | SRX9167469 | SRS7406196 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | S3 1 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:7|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | S3 1 | S3 1 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | S3_1_1.fq S3_1_2.fq | fastq fastq | 6903489600.0 | 69034896.0 | S3 1 1.fq | 0:100 1:100 | A:1984004671;C:1447920035;G:1460546712;T:2011018182;N:0 | 100 | 100 | 1984004671 | 1447920035 | 1460546712 | 2011018182 | 0 | SRX9167469 | SRS7406196 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.93549 | 0.20561 | 0.70569 | 0.53065 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61379 | 61379 | SRR12687504 | SRX9167468 | SRS7406195 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | Pre 3 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:6|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | Pre 3 | Pre 3 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | Pre_3_1.fq Pre_3_2.fq | fastq fastq | 7052506400.0 | 70525064.0 | Pre 3 1.fq | 0:100 1:100 | A:1970281685;C:1535313771;G:1548483633;T:1998427311;N:0 | 100 | 100 | 1970281685 | 1535313771 | 1548483633 | 1998427311 | 0 | SRX9167468 | SRS7406195 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.93825 | 0.16689 | 0.69071 | 0.5149 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61380 | 61380 | SRR12687505 | SRX9167467 | SRS7406194 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | Pre 2 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:5|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | Pre 2 | Pre 2 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | Pre_2_1.fq Pre_2_2.fq | fastq fastq | 6917153000.0 | 69171530.0 | Pre 2 1.fq | 0:100 1:100 | A:1954028740;C:1484690033;G:1500546828;T:1977887399;N:0 | 100 | 100 | 1954028740 | 1484690033 | 1500546828 | 1977887399 | 0 | SRX9167467 | SRS7406194 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.93653 | 0.18216 | 0.6939 | 0.50553 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61381 | 61381 | SRR12687506 | SRX9167466 | SRS7406193 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | Pre 1 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:4|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | Pre 1 | Pre 1 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | Pre_1_1.fq Pre_1_2.fq | fastq fastq | 7121559800.0 | 71215598.0 | Pre 1 1.fq | 0:100 1:100 | A:2016438936;C:1525107488;G:1542345073;T:2037668303;N:0 | 100 | 100 | 2016438936 | 1525107488 | 1542345073 | 2037668303 | 0 | SRX9167466 | SRS7406193 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.93748 | 0.18677 | 0.69234 | 0.51095 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61382 | 61382 | SRR12687507 | SRX9167465 | SRS7406192 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | Ctrl 3 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:3|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | Ctrl 3 | Ctrl 3 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | Ctrl_3_1.fq Ctrl_3_2.fq | fastq fastq | 6901468000.0 | 69014680.0 | Ctrl 3 1.fq | 0:100 1:100 | A:1958667379;C:1474001137;G:1490669190;T:1978130294;N:0 | 100 | 100 | 1958667379 | 1474001137 | 1490669190 | 1978130294 | 0 | SRX9167465 | SRS7406192 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.93909 | 0.19338 | 0.71021 | 0.5203 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61383 | 61383 | SRR12687508 | SRX9167464 | SRS7406191 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | ECH 3 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:15|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | ECH 3 | ECH 3 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | ECH_3_1.fq ECH_3_2.fq | fastq fastq | 6337825200.0 | 63378252.0 | ECH 3 1.fq | 0:100 1:100 | A:1737819108;C:1411890760;G:1450506396;T:1737608936;N:0 | 100 | 100 | 1737819108 | 1411890760 | 1450506396 | 1737608936 | 0 | SRX9167464 | SRS7406191 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.91909 | 0.14386 | 0.69526 | 0.46915 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61384 | 61384 | SRR12687509 | SRX9167463 | SRS7406190 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | ECH 2 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:14|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | ECH 2 | ECH 2 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | ECH_2_1.fq ECH_2_2.fq | fastq fastq | 6082199400.0 | 60821994.0 | ECH 2 1.fq | 0:100 1:100 | A:1665545787;C:1356011539;G:1398853438;T:1661788636;N:0 | 100 | 100 | 1665545787 | 1356011539 | 1398853438 | 1661788636 | 0 | SRX9167463 | SRS7406190 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.91909 | 0.13924 | 0.70019 | 0.47327 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61385 | 61385 | SRR12687510 | SRX9167462 | SRS7406189 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | ECH 1 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:13|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | ECH 1 | ECH 1 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | ECH_1_1.fq ECH_1_2.fq | fastq fastq | 6528165600.0 | 65281656.0 | ECH 1 1.fq | 0:100 1:100 | A:1756958748;C:1486036851;G:1521185932;T:1763984069;N:0 | 100 | 100 | 1756958748 | 1486036851 | 1521185932 | 1763984069 | 0 | SRX9167462 | SRS7406189 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.92456 | 0.1171 | 0.6858 | 0.48296 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61386 | 61386 | SRR12687511 | SRX9167461 | SRS7406188 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | AlCl3 3 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:12|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | AlCl3 3 | AlCl3 3 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | AlCl3_3_1.fq AlCl3_3_2.fq | fastq fastq | 6554672200.0 | 65546722.0 | AlCl3 3 1.fq | 0:100 1:100 | A:1789583657;C:1466854253;G:1506361550;T:1791872740;N:0 | 100 | 100 | 1789583657 | 1466854253 | 1506361550 | 1791872740 | 0 | SRX9167461 | SRS7406188 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.91837 | 0.13792 | 0.69199 | 0.46699 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61387 | 61387 | SRR12687512 | SRX9167460 | SRS7406187 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | AlCl3 2 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:11|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | AlCl3 2 | AlCl3 2 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | AlCl3_2_1.fq AlCl3_2_2.fq | fastq fastq | 6313522800.0 | 63135228.0 | AlCl3 2 1.fq | 0:100 1:100 | A:1703974139;C:1432828723;G:1472463459;T:1704256479;N:0 | 100 | 100 | 1703974139 | 1432828723 | 1472463459 | 1704256479 | 0 | SRX9167460 | SRS7406187 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.92027 | 0.12251 | 0.6913 | 0.46774 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61388 | 61388 | SRR12687513 | SRX9167459 | SRS7406186 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | Ctrl 2 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:2|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | Ctrl 2 | Ctrl 2 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | Ctrl_2_1.fq Ctrl_2_2.fq | fastq fastq | 7158573600.0 | 71585736.0 | Ctrl 2 1.fq | 0:100 1:100 | A:2037477785;C:1523658736;G:1537763707;T:2059673372;N:0 | 100 | 100 | 2037477785 | 1523658736 | 1537763707 | 2059673372 | 0 | SRX9167459 | SRS7406186 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.93876 | 0.19782 | 0.71315 | 0.52076 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 61389 | 61389 | SRR12687514 | SRX9167458 | SRS7406185 | SRP284444 | PRJNA664479 | RNA sequencing of transcriptome in zebrafish larvae | PRJNA664479 | Other | Study the potential signaling pathways of echinacoside treating osteoporosis and Alzheimer's disease by RNA sequencing based transcriptome in zebrafish larvae. | Ctrl 1 | host:missing|isolation source:zebrafish larvae|collection date:2019 03 20|geo loc name:China: Nanjing|lat lon:missing|tmp:1|age:missing|breed:missing|cultivar:missing|dev stage:missing|ecotype:missing|isolate:missing|sex:missing|strain:missing|tissue:missing|BioSampleModel:Model organism or animal | transcriptome | Ctrl 1 | Ctrl 1 | RNA sequencing | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP284444 | Ctrl_1_1.fq Ctrl_1_2.fq | fastq fastq | 7128907800.0 | 71289078.0 | Ctrl 1 1.fq | 0:100 1:100 | A:2024706079;C:1521330507;G:1536206815;T:2046664399;N:0 | 100 | 100 | 2024706079 | 1521330507 | 1536206815 | 2046664399 | 0 | SRX9167458 | SRS7406185 | SRA1129451 | China Pharmaceutical University|department of pharmacognosy | China Pharmaceutical University | 1 | 0.94262 | 0.19339 | 0.71522 | 0.43982 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2020-09-21 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 63586 | 63586 | SRR13951240 | SRX10330055 | SRS8449856 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT acrolein treated rep6 | GSM5169491 | source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae | Zebrafish larvae WT acrolein treated rep6 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT acrolein treated larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Acrolein|tissue:Larvae | GSM5169491 | GSM5169491: Zebrafish larvae WT acrolein treated rep6; Danio rerio; RNA Seq | GSM5169491 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169491 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAALRAAPEI-515_1.fq.gz V300079388_L3_HK500ZEBaopEAALRAAPEI-515_2.fq.gz | fastq fastq | 4980022200.0 | 49800222.0 | GSM5169491 r1 | 0:100 1:100 | A:1333773139;C:1140685596;G:1152592074;T:1352971391;N:0 | 100 | 100 | 1333773139 | 1140685596 | 1152592074 | 1352971391 | 0 | SRX10330055 | SRS8449856 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.9486 | 0.11229 | 0.65967 | 0.47337 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63587 | 63587 | SRR13951239 | SRX10330054 | SRS8449858 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT acrolein treated rep5 | GSM5169490 | source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae | Zebrafish larvae WT acrolein treated rep5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT acrolein treated larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Acrolein|tissue:Larvae | GSM5169490 | GSM5169490: Zebrafish larvae WT acrolein treated rep5; Danio rerio; RNA Seq | GSM5169490 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169490 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAAKRAAPEI-514_1.fq.gz V300079388_L3_HK500ZEBaopEAAKRAAPEI-514_2.fq.gz | fastq fastq | 4989256800.0 | 49892568.0 | GSM5169490 r1 | 0:100 1:100 | A:1333967860;C:1145275940;G:1156212626;T:1353800374;N:0 | 100 | 100 | 1333967860 | 1145275940 | 1156212626 | 1353800374 | 0 | SRX10330054 | SRS8449858 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94949 | 0.10728 | 0.65756 | 0.47006 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63588 | 63588 | SRR13951238 | SRX10330053 | SRS8449857 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT acrolein treated rep4 | GSM5169489 | source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae | Zebrafish larvae WT acrolein treated rep4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT acrolein treated larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Acrolein|tissue:Larvae | GSM5169489 | GSM5169489: Zebrafish larvae WT acrolein treated rep4; Danio rerio; RNA Seq | GSM5169489 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169489 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAAJRAAPEI-513_1.fq.gz V300079388_L3_HK500ZEBaopEAAJRAAPEI-513_2.fq.gz | fastq fastq | 4991600600.0 | 49916006.0 | GSM5169489 r1 | 0:100 1:100 | A:1332160517;C:1148004219;G:1159807037;T:1351628827;N:0 | 100 | 100 | 1332160517 | 1148004219 | 1159807037 | 1351628827 | 0 | SRX10330053 | SRS8449857 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.95038 | 0.10485 | 0.65977 | 0.47668 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63589 | 63589 | SRR13951237 | SRX10330052 | SRS8449855 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT acrolein treated rep3 | GSM5169488 | source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae | Zebrafish larvae WT acrolein treated rep3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT acrolein treated larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Acrolein|tissue:Larvae | GSM5169488 | GSM5169488: Zebrafish larvae WT acrolein treated rep3; Danio rerio; RNA Seq | GSM5169488 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169488 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAAIRAAPEI-512_1.fq.gz V300079388_L2_HK500ZEBaopEAAIRAAPEI-512_2.fq.gz | fastq fastq | 4931029800.0 | 49310298.0 | GSM5169488 r1 | 0:100 1:100 | A:1313566945;C:1137259809;G:1149091650;T:1331111396;N:0 | 100 | 100 | 1313566945 | 1137259809 | 1149091650 | 1331111396 | 0 | SRX10330052 | SRS8449855 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.95011 | 0.10594 | 0.65711 | 0.48179 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63590 | 63590 | SRR13951236 | SRX10330051 | SRS8449854 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT acrolein treated rep2 | GSM5169487 | source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae | Zebrafish larvae WT acrolein treated rep2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT acrolein treated larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Acrolein|tissue:Larvae | GSM5169487 | GSM5169487: Zebrafish larvae WT acrolein treated rep2; Danio rerio; RNA Seq | GSM5169487 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169487 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAAHRAAPEI-511_1.fq.gz V300079388_L2_HK500ZEBaopEAAHRAAPEI-511_2.fq.gz | fastq fastq | 4934978600.0 | 49349786.0 | GSM5169487 r1 | 0:100 1:100 | A:1318738318;C:1133208442;G:1143616038;T:1339415802;N:0 | 100 | 100 | 1318738318 | 1133208442 | 1143616038 | 1339415802 | 0 | SRX10330051 | SRS8449854 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.948 | 0.10568 | 0.65685 | 0.45325 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63591 | 63591 | SRR13951235 | SRX10330050 | SRS8449851 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT acrolein treated rep1 | GSM5169486 | source name:Zebrafish larvae WT acrolein treated larvae|genotype:WT|treatment:Acrolein|tissue:Larvae | Zebrafish larvae WT acrolein treated rep1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT acrolein treated larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Acrolein|tissue:Larvae | GSM5169486 | GSM5169486: Zebrafish larvae WT acrolein treated rep1; Danio rerio; RNA Seq | GSM5169486 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169486 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAAGRAAPEI-507_1.fq.gz V300079388_L2_HK500ZEBaopEAAGRAAPEI-507_2.fq.gz | fastq fastq | 4916868000.0 | 49168680.0 | GSM5169486 r1 | 0:100 1:100 | A:1319311116;C:1122812867;G:1129767432;T:1344976585;N:0 | 100 | 100 | 1319311116 | 1122812867 | 1129767432 | 1344976585 | 0 | SRX10330050 | SRS8449851 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94789 | 0.10769 | 0.65537 | 0.47629 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63592 | 63592 | SRR13951234 | SRX10330049 | SRS8449853 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT rep6 | GSM5169485 | source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae | Zebrafish larvae WT rep6 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Ctrl|tissue:Larvae | GSM5169485 | GSM5169485: Zebrafish larvae WT rep6; Danio rerio; RNA Seq | GSM5169485 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169485 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAAFRAAPEI-506_1.fq.gz V300079388_L2_HK500ZEBaopEAAFRAAPEI-506_2.fq.gz | fastq fastq | 4918223600.0 | 49182236.0 | GSM5169485 r1 | 0:100 1:100 | A:1312501446;C:1129859893;G:1141743360;T:1334118901;N:0 | 100 | 100 | 1312501446 | 1129859893 | 1141743360 | 1334118901 | 0 | SRX10330049 | SRS8449853 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94736 | 0.10854 | 0.66095 | 0.46684 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63593 | 63593 | SRR13951251 | SRX10330048 | SRS8449849 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT rep5 | GSM5169484 | source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae | Zebrafish larvae WT rep5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Ctrl|tissue:Larvae | GSM5169484 | GSM5169484: Zebrafish larvae WT rep5; Danio rerio; RNA Seq | GSM5169484 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169484 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAAERAAPEI-505_1.fq.gz V300079388_L2_HK500ZEBaopEAAERAAPEI-505_2.fq.gz | fastq fastq | 4921487400.0 | 49214874.0 | GSM5169484 r1 | 0:100 1:100 | A:1307773420;C:1137100007;G:1147334476;T:1329279497;N:0 | 100 | 100 | 1307773420 | 1137100007 | 1147334476 | 1329279497 | 0 | SRX10330048 | SRS8449849 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.9488 | 0.10243 | 0.65596 | 0.47526 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63594 | 63594 | SRR13951250 | SRX10330047 | SRS8449847 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT rep4 | GSM5169483 | source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae | Zebrafish larvae WT rep4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Ctrl|tissue:Larvae | GSM5169483 | GSM5169483: Zebrafish larvae WT rep4; Danio rerio; RNA Seq | GSM5169483 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169483 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAADRAAPEI-504_1.fq.gz V300079388_L2_HK500ZEBaopEAADRAAPEI-504_2.fq.gz | fastq fastq | 4902200200.0 | 49022002.0 | GSM5169483 r1 | 0:100 1:100 | A:1302490426;C:1131663107;G:1148042501;T:1320004166;N:0 | 100 | 100 | 1302490426 | 1131663107 | 1148042501 | 1320004166 | 0 | SRX10330047 | SRS8449847 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.9486 | 0.10416 | 0.66133 | 0.45959 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63595 | 63595 | SRR13951249 | SRX10330046 | SRS8449846 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT rep3 | GSM5169482 | source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae | Zebrafish larvae WT rep3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Ctrl|tissue:Larvae | GSM5169482 | GSM5169482: Zebrafish larvae WT rep3; Danio rerio; RNA Seq | GSM5169482 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169482 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAACRAAPEI-503_1.fq.gz V300079388_L2_HK500ZEBaopEAACRAAPEI-503_2.fq.gz | fastq fastq | 4932506000.0 | 49325060.0 | GSM5169482 r1 | 0:100 1:100 | A:1314021251;C:1136250372;G:1148046464;T:1334187913;N:0 | 100 | 100 | 1314021251 | 1136250372 | 1148046464 | 1334187913 | 0 | SRX10330046 | SRS8449846 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.95001 | 0.10334 | 0.66003 | 0.474 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63596 | 63596 | SRR13951248 | SRX10330045 | SRS8449848 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT rep2 | GSM5169481 | source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae | Zebrafish larvae WT rep2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Ctrl|tissue:Larvae | GSM5169481 | GSM5169481: Zebrafish larvae WT rep2; Danio rerio; RNA Seq | GSM5169481 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169481 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAABRAAPEI-502_1.fq.gz V300079388_L2_HK500ZEBaopEAABRAAPEI-502_2.fq.gz | fastq fastq | 4938494000.0 | 49384940.0 | GSM5169481 r1 | 0:100 1:100 | A:1313976068;C:1139517379;G:1153604159;T:1331396394;N:0 | 100 | 100 | 1313976068 | 1139517379 | 1153604159 | 1331396394 | 0 | SRX10330045 | SRS8449848 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94864 | 0.10252 | 0.65957 | 0.47642 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63597 | 63597 | SRR13951247 | SRX10330044 | SRS8449845 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae WT rep1 | GSM5169480 | source name:Zebrafish larvae WT larvae|genotype:WT|treatment:Ctrl|tissue:Larvae | Zebrafish larvae WT rep1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae WT larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:WT|treatment:Ctrl|tissue:Larvae | GSM5169480 | GSM5169480: Zebrafish larvae WT rep1; Danio rerio; RNA Seq | GSM5169480 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169480 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L2_HK500ZEBaopEAAARAAPEI-501_1.fq.gz V300079388_L2_HK500ZEBaopEAAARAAPEI-501_2.fq.gz | fastq fastq | 4920498800.0 | 49204988.0 | GSM5169480 r1 | 0:100 1:100 | A:1312070030;C:1133298664;G:1141858537;T:1333271569;N:0 | 100 | 100 | 1312070030 | 1133298664 | 1141858537 | 1333271569 | 0 | SRX10330044 | SRS8449845 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94865 | 0.10459 | 0.65965 | 0.46788 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63598 | 63598 | SRR13951246 | SRX10330043 | SRS8449844 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae akr1a1a KO rep6 | GSM5169479 | source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | Zebrafish larvae akr1a1a KO rep6 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae akr1a1a KO larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | GSM5169479 | GSM5169479: Zebrafish larvae akr1a1a KO rep6; Danio rerio; RNA Seq | GSM5169479 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169479 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAARRAAPEI-521_1.fq.gz V300079388_L3_HK500ZEBaopEAARRAAPEI-521_2.fq.gz | fastq fastq | 4983441000.0 | 49834410.0 | GSM5169479 r1 | 0:100 1:100 | A:1322739180;C:1153664354;G:1168919194;T:1338118272;N:0 | 100 | 100 | 1322739180 | 1153664354 | 1168919194 | 1338118272 | 0 | SRX10330043 | SRS8449844 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.9473 | 0.09632 | 0.66419 | 0.46649 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63599 | 63599 | SRR13951245 | SRX10330042 | SRS8449843 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae akr1a1a KO rep5 | GSM5169478 | source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | Zebrafish larvae akr1a1a KO rep5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae akr1a1a KO larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | GSM5169478 | GSM5169478: Zebrafish larvae akr1a1a KO rep5; Danio rerio; RNA Seq | GSM5169478 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169478 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAAQRAAPEI-520_1.fq.gz V300079388_L3_HK500ZEBaopEAAQRAAPEI-520_2.fq.gz | fastq fastq | 4979727600.0 | 49797276.0 | GSM5169478 r1 | 0:100 1:100 | A:1324141918;C:1150666829;G:1165518713;T:1339400140;N:0 | 100 | 100 | 1324141918 | 1150666829 | 1165518713 | 1339400140 | 0 | SRX10330042 | SRS8449843 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94914 | 0.09649 | 0.66377 | 0.47093 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63600 | 63600 | SRR13951244 | SRX10330041 | SRS8449852 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae akr1a1a KO rep4 | GSM5169477 | source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | Zebrafish larvae akr1a1a KO rep4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae akr1a1a KO larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | GSM5169477 | GSM5169477: Zebrafish larvae akr1a1a KO rep4; Danio rerio; RNA Seq | GSM5169477 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169477 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAAPRAAPEI-519_1.fq.gz V300079388_L3_HK500ZEBaopEAAPRAAPEI-519_2.fq.gz | fastq fastq | 4978998800.0 | 49789988.0 | GSM5169477 r1 | 0:100 1:100 | A:1333355936;C:1140285632;G:1151126213;T:1354231019;N:0 | 100 | 100 | 1333355936 | 1140285632 | 1151126213 | 1354231019 | 0 | SRX10330041 | SRS8449852 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94594 | 0.10032 | 0.66194 | 0.48009 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63601 | 63601 | SRR13951243 | SRX10330040 | SRS8449842 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae akr1a1a KO rep3 | GSM5169476 | source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | Zebrafish larvae akr1a1a KO rep3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae akr1a1a KO larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | GSM5169476 | GSM5169476: Zebrafish larvae akr1a1a KO rep3; Danio rerio; RNA Seq | GSM5169476 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169476 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAAORAAPEI-518_1.fq.gz V300079388_L3_HK500ZEBaopEAAORAAPEI-518_2.fq.gz | fastq fastq | 4978639200.0 | 49786392.0 | GSM5169476 r1 | 0:100 1:100 | A:1331238273;C:1143633964;G:1152228372;T:1351538591;N:0 | 100 | 100 | 1331238273 | 1143633964 | 1152228372 | 1351538591 | 0 | SRX10330040 | SRS8449842 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94616 | 0.1007 | 0.66054 | 0.46712 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63602 | 63602 | SRR13951242 | SRX10330039 | SRS8449850 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae akr1a1a KO rep2 | GSM5169475 | source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | Zebrafish larvae akr1a1a KO rep2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae akr1a1a KO larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | GSM5169475 | GSM5169475: Zebrafish larvae akr1a1a KO rep2; Danio rerio; RNA Seq | GSM5169475 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169475 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAANRAAPEI-517_1.fq.gz V300079388_L3_HK500ZEBaopEAANRAAPEI-517_2.fq.gz | fastq fastq | 4967553600.0 | 49675536.0 | GSM5169475 r1 | 0:100 1:100 | A:1324408005;C:1143569026;G:1158003192;T:1341573377;N:0 | 100 | 100 | 1324408005 | 1143569026 | 1158003192 | 1341573377 | 0 | SRX10330039 | SRS8449850 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94688 | 0.09559 | 0.66158 | 0.4794 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 63603 | 63603 | SRR13951241 | SRX10330038 | SRS8449841 | SRP310389 | PRJNA713989 | Next Generation Sequencing Facilitates Quantitative Analysis of Wildtype akr1a1a / and Wildtype with Acrolein Treatment Zebrafish Larvae Transcriptomes | GSE168786 | Transcriptome Analysis | Our previous experiments showed the function of Akr1a1a was related to insulin resistance. The knockout of Akr1a1a led to poor acrolein detoxification and accumulated acrolein inhibits insulin receptors insra/insrb expression. To understand how the loss of Akr1a1a and acrolein reflects at the transcriptome level we performed full genome RNA Seq between akr1a1a+/+ akr1a1a / and akr1a1a+/+ with acrolein treatment zebrafish larvae at 120 hpf. An overview of RNA Seq including quality control principal component analysis PCA and volcano plots of regulated genes showed comparable properties between akr1a1a mutants wild type and acrolein treated wild type zebrafish larvae. We found the insulin receptor signaling pathway was down regulated significantly in akr1a1a mutants and acrolein treated wild type larvae as compared to wild type larvae via gene set enrichment analysis normalized enrichment score 1.888 p=0.028; 1.93 p=0.019. Intriguingly downstream signaling pathways including MAPK signal transduction by protein phosphorylation and transmembrane receptor protein tyrosine kinase signaling pathway were also significantly down regulated in akr1a1a mutants and acrolein treated wild type larvae. Taken together these results further suggest akr1a1a and acrolein as an important regulator in insulin receptor signaling transduction. Furthermore we offer a comprehensive and more detailed evaluation of mRNA content within zebrafish larvae. We conclude that RNA seq based transcriptome would clearly illustrate genetic network and clarify complex biological functions. Overall design: mRNA expression profiles of wildtype akr1a1a / and wildtype with acrolein treatment zebrafish larvae at 120 hpf | pubmed:34278746;pubmed:36711148 | Zebrafish larvae akr1a1a KO rep1 | GSM5169474 | source name:Zebrafish larvae akr1a1a KO larvae|genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | Zebrafish larvae akr1a1a KO rep1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | Zebrafish larvae akr1a1a KO larvae | 6 replicates were treated with acrolein from 24 hpf to 120 hpf | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | Larvae were kept in E3 media at 28.5◦C with 10% PTU to suppress pigmentation formation. | genotype:akr1a1a KO|treatment:Ctrl|tissue:Larvae | GSM5169474 | GSM5169474: Zebrafish larvae akr1a1a KO rep1; Danio rerio; RNA Seq | GSM5169474 | 1 | Larvae were collected flash frozen on dry ice and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Cat#FC 122 1001 was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5169474 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP310389 | V300079388_L3_HK500ZEBaopEAAMRAAPEI-516_1.fq.gz V300079388_L3_HK500ZEBaopEAAMRAAPEI-516_2.fq.gz | fastq fastq | 4967500800.0 | 49675008.0 | GSM5169474 r1 | 0:100 1:100 | A:1323753410;C:1144795675;G:1158403216;T:1340548499;N:0 | 100 | 100 | 1323753410 | 1144795675 | 1158403216 | 1340548499 | 0 | SRX10330038 | SRS8449841 | SRA1205863 | GEO | ZMF, University Heidelberg | 1 | 0.94765 | 0.09715 | 0.66018 | 0.4542 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2021-03-12 | Multi-stage | Multi-stage | Undetermined | Undetermined | ||||||||||||||||
| 66964 | 66964 | SRR16965143 | SRX13156592 | SRS11088496 | SRP346547 | PRJNA780808 | transcriptomics of carbendazim and enrofloxacin on zebrafish embryos | PRJNA780808 | Other | reveal a interaction between ENF and CAR on metabolic regulation during development | 1mix | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:10 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio :mixture group | mix 1 | mix 1 | 96hpf zebrafish larvae mixture group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346547 | mix2_1_2.fq.gz | fastq | 3313823250.0 | 22092155.0 | mix2 1 2.fq.gz | 0:0 1:150 | A:895726357;C:763402657;G:745765587;T:908922686;N:5963 | 0 | 150 | 895726357 | 763402657 | 745765587 | 908922686 | 5963 | SRX13156592 | SRS11088496 | SRA1329868 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.93604 | 0.10794 | 0.65587 | 0.47956 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-17 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66965 | 66965 | SRR16965144 | SRX13156591 | SRS11088495 | SRP346547 | PRJNA780808 | transcriptomics of carbendazim and enrofloxacin on zebrafish embryos | PRJNA780808 | Other | reveal a interaction between ENF and CAR on metabolic regulation during development | 3enf | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:9 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio :enrofloxacin group | enf 3 | enf 3 | 96hpf zebrafish larvae enrofloxacin group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346547 | enf_3.fq.gz | fastq | 3304972350.0 | 22033149.0 | enf 3.fq.gz | 0:150 1:0 | A:899427202;C:745999066;G:759917309;T:899625137;N:3636 | 150 | 0 | 899427202 | 745999066 | 759917309 | 899625137 | 3636 | SRX13156591 | SRS11088495 | SRA1329868 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.94353 | 0.10795 | 0.66212 | 0.47773 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-17 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66966 | 66966 | SRR16965145 | SRX13156590 | SRS11088493 | SRP346547 | PRJNA780808 | transcriptomics of carbendazim and enrofloxacin on zebrafish embryos | PRJNA780808 | Other | reveal a interaction between ENF and CAR on metabolic regulation during development | 1enf | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:7 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio :enrofloxacin group | enf 1 | enf 1 | 96hpf zebrafish larvae enrofloxacin group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP346547 | enf_1.fq.gz enf_2.fq.gz | fastq fastq | 6652389300.0 | 44349262.0 | enf 1.fq.gz | 0:150 1:150 | A:1759651033;C:1563446116;G:1556912596;T:1772370048;N:9507 | 150 | 150 | 1759651033 | 1563446116 | 1556912596 | 1772370048 | 9507 | SRX13156590 | SRS11088493 | SRA1329868 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.94992 | 0.06316 | 0.66979 | 0.48987 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-17 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66967 | 66967 | SRR16965146 | SRX13156589 | SRS11088492 | SRP346547 | PRJNA780808 | transcriptomics of carbendazim and enrofloxacin on zebrafish embryos | PRJNA780808 | Other | reveal a interaction between ENF and CAR on metabolic regulation during development | 3car | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio :carbendazim group | car 3 | car 3 | 96hpf zebrafish larvae carbendazim group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346547 | car_3_1.fq.gz | fastq | 3335622150.0 | 22237481.0 | car 3 1.fq.gz | 0:150 1:0 | A:853229671;C:807433601;G:820478265;T:854475092;N:5521 | 150 | 0 | 853229671 | 807433601 | 820478265 | 854475092 | 5521 | SRX13156589 | SRS11088492 | SRA1329868 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.96567 | 0.03093 | 0.70997 | 0.47751 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-17 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66968 | 66968 | SRR16965147 | SRX13156588 | SRS11088494 | SRP346547 | PRJNA780808 | transcriptomics of carbendazim and enrofloxacin on zebrafish embryos | PRJNA780808 | Other | reveal a interaction between ENF and CAR on metabolic regulation during development | 1car | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:4 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio :carbendazim group | car 1 | car 1 | 96hpf zebrafish larvae carbendazim group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346547 | car_1_1.fq.gz | fastq | 3378056400.0 | 22520376.0 | car 1 1.fq.gz | 0:150 1:0 | A:886009175;C:795203398;G:809447342;T:887390300;N:6185 | 150 | 0 | 886009175 | 795203398 | 809447342 | 887390300 | 6185 | SRX13156588 | SRS11088494 | SRA1329868 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.95701 | 0.05956 | 0.67836 | 0.4884 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-17 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66969 | 66969 | SRR16965148 | SRX13156587 | SRS11088491 | SRP346547 | PRJNA780808 | transcriptomics of carbendazim and enrofloxacin on zebrafish embryos | PRJNA780808 | Other | reveal a interaction between ENF and CAR on metabolic regulation during development | 3con | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:3 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio :control group | con 3 | con 3 | 96hpf zebrafish larvae control group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346547 | con_3_2.fq.gz | fastq | 3359054500.0 | 33590545.0 | con 3 2.fq.gz | 0:100 1:0 | A:914533337;C:755914202;G:773676246;T:914930715;N:0 | 100 | 0 | 914533337 | 755914202 | 773676246 | 914930715 | 0 | SRX13156587 | SRS11088491 | SRA1329868 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.95076 | 0.10478 | 0.65646 | 0.49594 | 100 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-17 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66970 | 66970 | SRR16965149 | SRX13156586 | SRS11088489 | SRP346547 | PRJNA780808 | transcriptomics of carbendazim and enrofloxacin on zebrafish embryos | PRJNA780808 | Other | reveal a interaction between ENF and CAR on metabolic regulation during development | 3mix | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:12 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio :mixture group | mix 3 | mix 3 | 96hpf zebrafish larvae mixture group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346547 | mix2_3_1.fq.gz | fastq | 3362094000.0 | 33620940.0 | mix2 3 1.fq.gz | 0:100 1:0 | A:916124379;C:755910593;G:768246534;T:921812494;N:0 | 100 | 0 | 916124379 | 755910593 | 768246534 | 921812494 | 0 | SRX13156586 | SRS11088489 | SRA1329868 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.94894 | 0.10416 | 0.65342 | 0.49475 | 100 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-17 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66971 | 66971 | SRR16965150 | SRX13156585 | SRS11088490 | SRP346547 | PRJNA780808 | transcriptomics of carbendazim and enrofloxacin on zebrafish embryos | PRJNA780808 | Other | reveal a interaction between ENF and CAR on metabolic regulation during development | 2mix | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:11 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio :mixture group | mix 2 | mix 2 | 96hpf zebrafish larvae mixture group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP346547 | car_2_2.fq.gz mix2_2_1.fq.gz | fastq fastq | 6669719100.0 | 44464794.0 | car 2 2.fq.gz | 0:150 1:150 | A:1815824677;C:1515086864;G:1506360115;T:1832433148;N:14296 | 150 | 150 | 1815824677 | 1515086864 | 1506360115 | 1832433148 | 14296 | SRX13156585 | SRS11088490 | SRA1329868 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.93884 | 0.11657 | 0.65527 | 0.48114 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-17 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66972 | 66972 | SRR16965151 | SRX13156584 | SRS11088488 | SRP346547 | PRJNA780808 | transcriptomics of carbendazim and enrofloxacin on zebrafish embryos | PRJNA780808 | Other | reveal a interaction between ENF and CAR on metabolic regulation during development | 2con | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:2 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio :control group | con 2 | con 2 | 96hpf zebrafish larvae control group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346547 | loader:fastq load.py | con_2_2.fq | fastq | 3324287550.0 | 22161917.0 | con 2 2.fq.gz | 0:150 | A:848766265;C:812477645;G:798995610;T:864040426;N:7604 | 150 | 848766265 | 812477645 | 798995610 | 864040426 | 7604 | SRX13156584 | SRS11088488 | SRA1329868 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.95546 | 0.03524 | 0.70027 | 0.48649 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-22 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66973 | 66973 | SRR16965152 | SRX13156583 | SRS11088487 | SRP346547 | PRJNA780808 | transcriptomics of carbendazim and enrofloxacin on zebrafish embryos | PRJNA780808 | Other | reveal a interaction between ENF and CAR on metabolic regulation during development | 1con | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:1 96hpf|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio :control group | con 1 | con 1 | 96hpf zebrafish larvae control group | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346547 | loader:fastq load.py | con_1_1.fq | fastq | 3330724500.0 | 22204830.0 | con 1 1.fq.gz | 0:150 | A:896812508;C:762246067;G:774062043;T:897597946;N:5936 | 150 | 896812508 | 762246067 | 774062043 | 897597946 | 5936 | SRX13156583 | SRS11088487 | SRA1329868 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.94926 | 0.08711 | 0.66789 | 0.48628 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-22 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66974 | 66974 | SRR16959538 | SRX13151074 | SRS11083380 | SRP346418 | PRJNA780940 | transcriptomics of difenoconazole and dimethomorph on zebrafish embryos | PRJNA780940 | Other | Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples so the deleterious effects of combined exposure warrant detailed examination. In this study the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate deformity rate lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes cdk1 and cdc20 thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone. | 1+mix | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:10 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio : mixture group | mix 1 | mix 1 | The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP346418 | mix1_3_2.fq.gz mix1_1_1.fq.gz | fastq fastq | 6639699600.0 | 44264664.0 | mix1 1 1.fq.gz | 0:150 1:150 | A:1738687157;C:1575344731;G:1569683716;T:1755974708;N:9288 | 150 | 150 | 1738687157 | 1575344731 | 1569683716 | 1755974708 | 9288 | SRX13151074 | SRS11083380 | SRA1330365 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.95161 | 0.05697 | 0.6817 | 0.48485 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-16 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66975 | 66975 | SRR16959539 | SRX13151073 | SRS11083379 | SRP346418 | PRJNA780940 | transcriptomics of difenoconazole and dimethomorph on zebrafish embryos | PRJNA780940 | Other | Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples so the deleterious effects of combined exposure warrant detailed examination. In this study the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate deformity rate lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes cdk1 and cdc20 thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone. | 2dim | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:8 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio : dimethomorph group | dim 2 | dim 2 | The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346418 | dim_2_1.fq.gz | fastq | 3344257500.0 | 22295050.0 | dim 2 1.fq.gz | 0:150 1:0 | A:895700119;C:767415749;G:784994320;T:896143585;N:3727 | 150 | 0 | 895700119 | 767415749 | 784994320 | 896143585 | 3727 | SRX13151073 | SRS11083379 | SRA1330365 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.9497 | 0.08418 | 0.66352 | 0.49341 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-16 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66976 | 66976 | SRR16959540 | SRX13151072 | SRS11083378 | SRP346418 | PRJNA780940 | transcriptomics of difenoconazole and dimethomorph on zebrafish embryos | PRJNA780940 | Other | Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples so the deleterious effects of combined exposure warrant detailed examination. In this study the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate deformity rate lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes cdk1 and cdc20 thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone. | 1dim | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:7 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio : dimethomorph group | dim 1 | dim 1 | The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346418 | dim_1_1.fq.gz | fastq | 3318812250.0 | 22125415.0 | dim 1 1.fq.gz | 0:150 1:0 | A:908481293;C:742787936;G:755930542;T:911608821;N:3658 | 150 | 0 | 908481293 | 742787936 | 755930542 | 911608821 | 3658 | SRX13151072 | SRS11083378 | SRA1330365 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.94211 | 0.11824 | 0.65344 | 0.47716 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-16 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66977 | 66977 | SRR16959541 | SRX13151071 | SRS11083377 | SRP346418 | PRJNA780940 | transcriptomics of difenoconazole and dimethomorph on zebrafish embryos | PRJNA780940 | Other | Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples so the deleterious effects of combined exposure warrant detailed examination. In this study the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate deformity rate lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes cdk1 and cdc20 thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone. | 3dif | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:6 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio : difenoconazole group | dif 3 | dif 3 | The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346418 | dif_3_1.fq.gz | fastq | 3318453000.0 | 22123020.0 | dif 3 1.fq.gz | 0:150 1:0 | A:893975607;C:758489621;G:772391705;T:893592335;N:3732 | 150 | 0 | 893975607 | 758489621 | 772391705 | 893592335 | 3732 | SRX13151071 | SRS11083377 | SRA1330365 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.94838 | 0.08393 | 0.66543 | 0.4818 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-16 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66978 | 66978 | SRR16959542 | SRX13151070 | SRS11083376 | SRP346418 | PRJNA780940 | transcriptomics of difenoconazole and dimethomorph on zebrafish embryos | PRJNA780940 | Other | Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples so the deleterious effects of combined exposure warrant detailed examination. In this study the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate deformity rate lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes cdk1 and cdc20 thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone. | 2dif | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:5 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio : difenoconazole group | dif 2 | dif 2 | The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346418 | dif_2_2.fq.gz | fastq | 3304972350.0 | 22033149.0 | dif 2 2.fq.gz | 0:0 1:150 | A:890456734;C:764917766;G:744757536;T:904833787;N:6527 | 0 | 150 | 890456734 | 764917766 | 744757536 | 904833787 | 6527 | SRX13151070 | SRS11083376 | SRA1330365 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.93514 | 0.107 | 0.6633 | 0.47599 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-16 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66979 | 66979 | SRR16959543 | SRX13151069 | SRS11083375 | SRP346418 | PRJNA780940 | transcriptomics of difenoconazole and dimethomorph on zebrafish embryos | PRJNA780940 | Other | Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples so the deleterious effects of combined exposure warrant detailed examination. In this study the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate deformity rate lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes cdk1 and cdc20 thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone. | 1dif | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:4 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio : difenoconazole group | dif 1 | dif 1 | The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346418 | dif_1_1.fq.gz | fastq | 3295443900.0 | 21969626.0 | dif 1 1.fq.gz | 0:150 1:0 | A:887936493;C:751636494;G:765508757;T:890358629;N:3527 | 150 | 0 | 887936493 | 751636494 | 765508757 | 890358629 | 3527 | SRX13151069 | SRS11083375 | SRA1330365 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.94623 | 0.09138 | 0.66478 | 0.4828 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-16 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66980 | 66980 | SRR16959544 | SRX13151068 | SRS11083374 | SRP346418 | PRJNA780940 | transcriptomics of difenoconazole and dimethomorph on zebrafish embryos | PRJNA780940 | Other | Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples so the deleterious effects of combined exposure warrant detailed examination. In this study the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate deformity rate lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes cdk1 and cdc20 thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone. | 3+con | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:3 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio : control group | con 3 | con 3 | The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346418 | con_3_1.fq.gz | fastq | 3306406800.0 | 22042712.0 | con 3 1.fq.gz | 0:150 1:0 | A:872740236;C:773482184;G:788334419;T:871846539;N:3422 | 150 | 0 | 872740236 | 773482184 | 788334419 | 871846539 | 3422 | SRX13151068 | SRS11083374 | SRA1330365 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.95458 | 0.06103 | 0.67409 | 0.48439 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-16 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66981 | 66981 | SRR16959545 | SRX13151067 | SRS11083373 | SRP346418 | PRJNA780940 | transcriptomics of difenoconazole and dimethomorph on zebrafish embryos | PRJNA780940 | Other | Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples so the deleterious effects of combined exposure warrant detailed examination. In this study the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate deformity rate lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes cdk1 and cdc20 thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone. | 2+mix | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:11 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio : mixture group | mix 2 | mix 2 | The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | PAIRED | BGISEQ | BGISEQ-500 | SRP346418 | mix1_2_1.fq.gz dim_3_2.fq.gz | fastq fastq | 6589866900.0 | 43932446.0 | dim 3 2.fq.gz | 0:150 1:150 | A:1782755416;C:1508342477;G:1501934674;T:1796820276;N:14057 | 150 | 150 | 1782755416 | 1508342477 | 1501934674 | 1796820276 | 14057 | SRX13151067 | SRS11083373 | SRA1330365 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.93861 | 0.10685 | 0.66393 | 0.47194 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-16 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66982 | 66982 | SRR16959546 | SRX13151066 | SRS11083372 | SRP346418 | PRJNA780940 | transcriptomics of difenoconazole and dimethomorph on zebrafish embryos | PRJNA780940 | Other | Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples so the deleterious effects of combined exposure warrant detailed examination. In this study the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate deformity rate lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes cdk1 and cdc20 thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone. | 2+con | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:2 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio : control group | con 2 | con 2 | The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346418 | con_2_2.fq.gz | fastq | 3324287550.0 | 22161917.0 | con 2 2.fq.gz | 0:0 1:150 | A:848766265;C:812477645;G:798995610;T:864040426;N:7604 | 0 | 150 | 848766265 | 812477645 | 798995610 | 864040426 | 7604 | SRX13151066 | SRS11083372 | SRA1330365 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.95548 | 0.03524 | 0.70021 | 0.4867 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-16 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 66983 | 66983 | SRR16959547 | SRX13151065 | SRS11083371 | SRP346418 | PRJNA780940 | transcriptomics of difenoconazole and dimethomorph on zebrafish embryos | PRJNA780940 | Other | Difenoconazole DIF and dimethomorph DIM are widely used pesticides frequently detected together in environmental samples so the deleterious effects of combined exposure warrant detailed examination. In this study the individual and combined effects of DIM and DIF on conventional developmental parameters hatch rate deformity rate lethality and gene expression were measured in embryonic zebrafish. Both DIF and DIM interfered with normal zebrafish embryo development and the most sensitive toxicity index for both was 96 hpf deformity rate BMDL10 values of 0.30 and 1.10 mg/L respectively. The combination of DIF and DIM had mainly synergistic deleterious effects on 96 hpf deformity and mortality rates. Transcriptome analysis showed that these compounds markedly downregulated expression of mcm family genes cdk1 and cdc20 thereby potentially disrupting DNA replication and cell cycle progression. Enhanced surveillance for this pesticide combination is recommended as simultaneous environmental exposure may be substantially more harmful than exposure to either compound alone. | 1+con | strain:Tu|isolate:N/A|breed:N/A|cultivar:N/A|ecotype:N/A|age:1 96h|dev stage:larvae|sex:male and female|tissue:larvae|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio : control group | con 1 | con 1 | The final library was amplified with phi29 to make DNA nanoballs DNB with more than 300 copies of one molecular. | RNA-Seq | TRANSCRIPTOMIC | Oligo-dT | SINGLE | BGISEQ | BGISEQ-500 | SRP346418 | con_1_1.fq.gz | fastq | 3330724500.0 | 22204830.0 | con 1 1.fq.gz | 0:150 1:0 | A:896812508;C:762246067;G:774062043;T:897597946;N:5936 | 150 | 0 | 896812508 | 762246067 | 774062043 | 897597946 | 5936 | SRX13151065 | SRS11083371 | SRA1330365 | China Agricultural University|College of animal science and technology | China Agricultural University | 1 | 0.94925 | 0.08711 | 0.66772 | 0.48635 | 150 | B | usable mapping rate | bgi | bgi | unknown | poly_a | unknown | bulk | unknown | unknown | China | 2021-11-16 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 68473 | 68473 | SRR17793192 | SRX13955361 | SRS11795776 | SRP357103 | PRJNA801348 | Global studies of Nur77 on metabolism of zebrafish | PRJNA801348 | Other | We created a global Nur77 knockout zebrafish model by CRISPR/Cas9 technique and then performed the whole organism RNA sequencing analysis in wild type and nur77 deficient zebrafish to dissect the changes genes in metabolic related pathways. | WT3 | strain:WT replicate 3|age:6 dpf|sex:male and female|tissue:Total|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: 6 dpf larvea | Li lab Nur77 6 | Li lab Nur77 6 | There are two groups: WT and Nur77 mutant. Every group has three replicates. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | BGISEQ | BGISEQ-500 | SRP357103 | WT3.fq.gz | fastq | 1076798350.0 | 21535967.0 | WT3.fq.gz | 0:50 1:0 | A:290308649;C:238961327;G:249860004;T:297257553;N:410817 | 50 | 0 | 290308649 | 238961327 | 249860004 | 297257553 | 410817 | SRX13955361 | SRS11795776 | SRA1363249 | Xiamen University|School of pharmaceutical sciences | Xiamen University | 1 | 0.9388 | 0.12749 | 0.66087 | 0.4989 | 50 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2022-01-27 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 68474 | 68474 | SRR17793193 | SRX13955360 | SRS11795775 | SRP357103 | PRJNA801348 | Global studies of Nur77 on metabolism of zebrafish | PRJNA801348 | Other | We created a global Nur77 knockout zebrafish model by CRISPR/Cas9 technique and then performed the whole organism RNA sequencing analysis in wild type and nur77 deficient zebrafish to dissect the changes genes in metabolic related pathways. | WT2 | strain:WT replicate 2|age:6 dpf|sex:male and female|tissue:Total|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: 6 dpf larvea | Li lab Nur77 5 | Li lab Nur77 5 | There are two groups: WT and Nur77 mutant. Every group has three replicates. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | BGISEQ | BGISEQ-500 | SRP357103 | WT2.fq.gz | fastq | 1076181450.0 | 21523629.0 | WT2.fq.gz | 0:50 1:0 | A:289932885;C:238687076;G:249724577;T:297412345;N:424567 | 50 | 0 | 289932885 | 238687076 | 249724577 | 297412345 | 424567 | SRX13955360 | SRS11795775 | SRA1363249 | Xiamen University|School of pharmaceutical sciences | Xiamen University | 1 | 0.93932 | 0.1297 | 0.66038 | 0.48203 | 50 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2022-01-27 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 68475 | 68475 | SRR17793194 | SRX13955359 | SRS11795774 | SRP357103 | PRJNA801348 | Global studies of Nur77 on metabolism of zebrafish | PRJNA801348 | Other | We created a global Nur77 knockout zebrafish model by CRISPR/Cas9 technique and then performed the whole organism RNA sequencing analysis in wild type and nur77 deficient zebrafish to dissect the changes genes in metabolic related pathways. | WT1 | strain:WT replicate 1|age:6 dpf|sex:male and female|tissue:Total|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: 6 dpf larvea | Li lab Nur77 4 | Li lab Nur77 4 | There are two groups: WT and Nur77 mutant. Every group has three replicates. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | BGISEQ | BGISEQ-500 | SRP357103 | WT1.fq.gz | fastq | 1076191400.0 | 21523828.0 | WT1.fq.gz | 0:50 1:0 | A:291276889;C:238480546;G:249179972;T:296814696;N:439297 | 50 | 0 | 291276889 | 238480546 | 249179972 | 296814696 | 439297 | SRX13955359 | SRS11795774 | SRA1363249 | Xiamen University|School of pharmaceutical sciences | Xiamen University | 1 | 0.93825 | 0.12843 | 0.66119 | 0.49668 | 50 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2022-01-27 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 68476 | 68476 | SRR17793195 | SRX13955358 | SRS11795773 | SRP357103 | PRJNA801348 | Global studies of Nur77 on metabolism of zebrafish | PRJNA801348 | Other | We created a global Nur77 knockout zebrafish model by CRISPR/Cas9 technique and then performed the whole organism RNA sequencing analysis in wild type and nur77 deficient zebrafish to dissect the changes genes in metabolic related pathways. | nur77KO3 | strain:nur77KO replicate 3|age:6 dpf|sex:male and female|tissue:Total|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: 6 dpf larvea | Li lab Nur77 3 | Li lab Nur77 3 | There are two groups: WT and Nur77 mutant. Every group has three replicates. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | BGISEQ | BGISEQ-500 | SRP357103 | Nur773.fq.gz | fastq | 1076004450.0 | 21520089.0 | Nur773.fq.gz | 0:50 1:0 | A:290229363;C:238956151;G:246664664;T:299742511;N:411761 | 50 | 0 | 290229363 | 238956151 | 246664664 | 299742511 | 411761 | SRX13955358 | SRS11795773 | SRA1363249 | Xiamen University|School of pharmaceutical sciences | Xiamen University | 1 | 0.93696 | 0.13828 | 0.66397 | 0.48777 | 50 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2022-01-27 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 68477 | 68477 | SRR17793196 | SRX13955357 | SRS11795772 | SRP357103 | PRJNA801348 | Global studies of Nur77 on metabolism of zebrafish | PRJNA801348 | Other | We created a global Nur77 knockout zebrafish model by CRISPR/Cas9 technique and then performed the whole organism RNA sequencing analysis in wild type and nur77 deficient zebrafish to dissect the changes genes in metabolic related pathways. | nur77KO2 | strain:nur77KO replicate 2|age:6 dpf|sex:male and female|tissue:Total|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: 6 dpf larvea | Li lab Nur77 2 | Li lab Nur77 2 | There are two groups: WT and Nur77 mutant. Every group has three replicates. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | BGISEQ | BGISEQ-500 | SRP357103 | Nur772.fq.gz | fastq | 1075868050.0 | 21517361.0 | Nur772.fq.gz | 0:50 1:0 | A:288260097;C:241294246;G:250714084;T:295165628;N:433995 | 50 | 0 | 288260097 | 241294246 | 250714084 | 295165628 | 433995 | SRX13955357 | SRS11795772 | SRA1363249 | Xiamen University|School of pharmaceutical sciences | Xiamen University | 1 | 0.94112 | 0.11813 | 0.66582 | 0.48643 | 50 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2022-01-27 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 68478 | 68478 | SRR17793197 | SRX13955356 | SRS11795771 | SRP357103 | PRJNA801348 | Global studies of Nur77 on metabolism of zebrafish | PRJNA801348 | Other | We created a global Nur77 knockout zebrafish model by CRISPR/Cas9 technique and then performed the whole organism RNA sequencing analysis in wild type and nur77 deficient zebrafish to dissect the changes genes in metabolic related pathways. | nur77KO1 | strain:nur77KO replicate 1|age:6 dpf|sex:male and female|tissue:Total|BioSampleModel:Model organism or animal | RNA Seq of Danio rerio: 6 dpf larvea | Li lab Nur77 1 | Li lab Nur77 1 | There are two groups: WT and Nur77 mutant. Every group has three replicates. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | BGISEQ | BGISEQ-500 | SRP357103 | Nur771.fq.gz | fastq | 1075810450.0 | 21516209.0 | Nur771.fq.gz | 0:50 1:0 | A:287851992;C:241486200;G:251500529;T:294560911;N:410818 | 50 | 0 | 287851992 | 241486200 | 251500529 | 294560911 | 410818 | SRX13955356 | SRS11795771 | SRA1363249 | Xiamen University|School of pharmaceutical sciences | Xiamen University | 1 | 0.94193 | 0.11554 | 0.6676 | 0.49728 | 50 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2022-01-27 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||||||||||||
| 68838 | 68838 | SRR18210594 | SRX14357147 | SRS12170698 | SRP362286 | PRJNA812402 | Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3 / knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3] | GSE197826 | Transcriptome Analysis | Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1 Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1 elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1 / elmo2+/+ and elmo2 / and elmo3+/+ and elmo3 / zebrafish larvae at 120 hpf Here we provide the sequencing data of elmo3+/+ and elmo3 / . Overall design: Total RNA profiles of wildtype and homozygous elmo3 knockout zebrafish larvae samples | parent bioproject:PRJNA812396 | pubmed:35874819 | elmo3 / knockout rep6 | GSM5930979 | source name:30 zebrafish larvae|genotype/variation:elmo3|tissue:30 zebrafish larvae | elmo3 / knockout rep6 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | 30 zebrafish larvae | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype/variation:elmo3|tissue:30 zebrafish larvae | GSM5930979 | GSM5930979: elmo3 / knockout rep6; Danio rerio; RNA Seq | GSM5930979 r1 | GSM5930979 | 1 | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP362286 | K3I_1.fq.gz K3I_2.fq.gz | fastq fastq | 4198309400.0 | 41983094.0 | GSM5930979 r1 | 0:100 1:100 | A:1117699123;C:963385646;G:1002297605;T:1114927026;N:0 | 100 | 100 | 1117699123 | 963385646 | 1002297605 | 1114927026 | 0 | SRX14357147 | SRS12170698 | SRA1380529 | ZMF, University Heidelberg | ZMF, University Heidelberg | 1 | 0.95398 | 0.09893 | 0.68566 | 0.48384 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2022-03-03 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||
| 68839 | 68839 | SRR18210595 | SRX14357146 | SRS12170697 | SRP362286 | PRJNA812402 | Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3 / knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3] | GSE197826 | Transcriptome Analysis | Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1 Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1 elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1 / elmo2+/+ and elmo2 / and elmo3+/+ and elmo3 / zebrafish larvae at 120 hpf Here we provide the sequencing data of elmo3+/+ and elmo3 / . Overall design: Total RNA profiles of wildtype and homozygous elmo3 knockout zebrafish larvae samples | parent bioproject:PRJNA812396 | pubmed:35874819 | elmo3 / knockout rep5 | GSM5930978 | source name:30 zebrafish larvae|genotype/variation:elmo3|tissue:30 zebrafish larvae | elmo3 / knockout rep5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | 30 zebrafish larvae | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype/variation:elmo3|tissue:30 zebrafish larvae | GSM5930978 | GSM5930978: elmo3 / knockout rep5; Danio rerio; RNA Seq | GSM5930978 r1 | GSM5930978 | 1 | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP362286 | K3H_1.fq.gz K3H_2.fq.gz | fastq fastq | 4200293800.0 | 42002938.0 | GSM5930978 r1 | 0:100 1:100 | A:1111878794;C:972313858;G:1004784160;T:1111316988;N:0 | 100 | 100 | 1111878794 | 972313858 | 1004784160 | 1111316988 | 0 | SRX14357146 | SRS12170697 | SRA1380529 | ZMF, University Heidelberg | ZMF, University Heidelberg | 1 | 0.95476 | 0.08651 | 0.67996 | 0.49703 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2022-03-03 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||
| 68840 | 68840 | SRR18210596 | SRX14357145 | SRS12170696 | SRP362286 | PRJNA812402 | Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3 / knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3] | GSE197826 | Transcriptome Analysis | Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1 Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1 elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1 / elmo2+/+ and elmo2 / and elmo3+/+ and elmo3 / zebrafish larvae at 120 hpf Here we provide the sequencing data of elmo3+/+ and elmo3 / . Overall design: Total RNA profiles of wildtype and homozygous elmo3 knockout zebrafish larvae samples | parent bioproject:PRJNA812396 | pubmed:35874819 | elmo3 / knockout rep4 | GSM5930977 | source name:30 zebrafish larvae|genotype/variation:elmo3|tissue:30 zebrafish larvae | elmo3 / knockout rep4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | 30 zebrafish larvae | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype/variation:elmo3|tissue:30 zebrafish larvae | GSM5930977 | GSM5930977: elmo3 / knockout rep4; Danio rerio; RNA Seq | GSM5930977 r1 | GSM5930977 | 1 | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP362286 | K3G_1.fq.gz K3G_2.fq.gz | fastq fastq | 4199888000.0 | 41998880.0 | GSM5930977 r1 | 0:100 1:100 | A:1122334661;C:958264493;G:990841979;T:1128446867;N:0 | 100 | 100 | 1122334661 | 958264493 | 990841979 | 1128446867 | 0 | SRX14357145 | SRS12170696 | SRA1380529 | ZMF, University Heidelberg | ZMF, University Heidelberg | 1 | 0.95553 | 0.09574 | 0.67588 | 0.50546 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2022-03-03 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||
| 68841 | 68841 | SRR18210597 | SRX14357144 | SRS12170694 | SRP362286 | PRJNA812402 | Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3 / knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3] | GSE197826 | Transcriptome Analysis | Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1 Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1 elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1 / elmo2+/+ and elmo2 / and elmo3+/+ and elmo3 / zebrafish larvae at 120 hpf Here we provide the sequencing data of elmo3+/+ and elmo3 / . Overall design: Total RNA profiles of wildtype and homozygous elmo3 knockout zebrafish larvae samples | parent bioproject:PRJNA812396 | pubmed:35874819 | elmo3 / knockout rep3 | GSM5930976 | source name:30 zebrafish larvae|genotype/variation:elmo3|tissue:30 zebrafish larvae | elmo3 / knockout rep3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | 30 zebrafish larvae | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype/variation:elmo3|tissue:30 zebrafish larvae | GSM5930976 | GSM5930976: elmo3 / knockout rep3; Danio rerio; RNA Seq | GSM5930976 r1 | GSM5930976 | 1 | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP362286 | K3F_1.fq.gz K3F_2.fq.gz | fastq fastq | 4199826800.0 | 41998268.0 | GSM5930976 r1 | 0:100 1:100 | A:1114418423;C:970590366;G:1007129552;T:1107688459;N:0 | 100 | 100 | 1114418423 | 970590366 | 1007129552 | 1107688459 | 0 | SRX14357144 | SRS12170694 | SRA1380529 | ZMF, University Heidelberg | ZMF, University Heidelberg | 1 | 0.95603 | 0.09095 | 0.68674 | 0.50452 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2022-03-03 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||
| 68842 | 68842 | SRR18210598 | SRX14357143 | SRS12170695 | SRP362286 | PRJNA812402 | Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3 / knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3] | GSE197826 | Transcriptome Analysis | Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1 Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1 elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1 / elmo2+/+ and elmo2 / and elmo3+/+ and elmo3 / zebrafish larvae at 120 hpf Here we provide the sequencing data of elmo3+/+ and elmo3 / . Overall design: Total RNA profiles of wildtype and homozygous elmo3 knockout zebrafish larvae samples | parent bioproject:PRJNA812396 | pubmed:35874819 | elmo3 / knockout rep2 | GSM5930975 | source name:30 zebrafish larvae|genotype/variation:elmo3|tissue:30 zebrafish larvae | elmo3 / knockout rep2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | 30 zebrafish larvae | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype/variation:elmo3|tissue:30 zebrafish larvae | GSM5930975 | GSM5930975: elmo3 / knockout rep2; Danio rerio; RNA Seq | GSM5930975 r1 | GSM5930975 | 1 | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP362286 | K3E_1.fq.gz K3E_2.fq.gz | fastq fastq | 4200209800.0 | 42002098.0 | GSM5930975 r1 | 0:100 1:100 | A:1126832572;C:958243133;G:992875301;T:1122258794;N:0 | 100 | 100 | 1126832572 | 958243133 | 992875301 | 1122258794 | 0 | SRX14357143 | SRS12170695 | SRA1380529 | ZMF, University Heidelberg | ZMF, University Heidelberg | 1 | 0.95571 | 0.09876 | 0.6925 | 0.50236 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2022-03-03 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||
| 68843 | 68843 | SRR18210599 | SRX14357142 | SRS12170692 | SRP362286 | PRJNA812402 | Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3 / knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3] | GSE197826 | Transcriptome Analysis | Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1 Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1 elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1 / elmo2+/+ and elmo2 / and elmo3+/+ and elmo3 / zebrafish larvae at 120 hpf Here we provide the sequencing data of elmo3+/+ and elmo3 / . Overall design: Total RNA profiles of wildtype and homozygous elmo3 knockout zebrafish larvae samples | parent bioproject:PRJNA812396 | pubmed:35874819 | elmo3 / knockout rep1 | GSM5930974 | source name:30 zebrafish larvae|genotype/variation:elmo3|tissue:30 zebrafish larvae | elmo3 / knockout rep1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | 30 zebrafish larvae | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype/variation:elmo3|tissue:30 zebrafish larvae | GSM5930974 | GSM5930974: elmo3 / knockout rep1; Danio rerio; RNA Seq | GSM5930974 r1 | GSM5930974 | 1 | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP362286 | K3D_1.fq.gz K3D_2.fq.gz | fastq fastq | 4199924600.0 | 41999246.0 | GSM5930974 r1 | 0:100 1:100 | A:1113558486;C:971352671;G:1006070235;T:1108943208;N:0 | 100 | 100 | 1113558486 | 971352671 | 1006070235 | 1108943208 | 0 | SRX14357142 | SRS12170692 | SRA1380529 | ZMF, University Heidelberg | ZMF, University Heidelberg | 1 | 0.9574 | 0.09203 | 0.68343 | 0.50108 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2022-03-03 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||
| 68844 | 68844 | SRR18210600 | SRX14357141 | SRS12170691 | SRP362286 | PRJNA812402 | Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3 / knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3] | GSE197826 | Transcriptome Analysis | Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1 Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1 elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1 / elmo2+/+ and elmo2 / and elmo3+/+ and elmo3 / zebrafish larvae at 120 hpf Here we provide the sequencing data of elmo3+/+ and elmo3 / . Overall design: Total RNA profiles of wildtype and homozygous elmo3 knockout zebrafish larvae samples | parent bioproject:PRJNA812396 | pubmed:35874819 | elmo3+/+ wildtype rep6 | GSM5930973 | source name:30 zebrafish larvae|genotype/variation:WT|tissue:30 zebrafish larvae | elmo3+/+ wildtype rep6 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | 30 zebrafish larvae | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype/variation:WT|tissue:30 zebrafish larvae | GSM5930973 | GSM5930973: elmo3+/+ wildtype rep6; Danio rerio; RNA Seq | GSM5930973 r1 | GSM5930973 | 1 | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP362286 | K39_1.fq.gz K39_2.fq.gz | fastq fastq | 4200212200.0 | 42002122.0 | GSM5930973 r1 | 0:100 1:100 | A:1104030091;C:980101129;G:1016311397;T:1099769583;N:0 | 100 | 100 | 1104030091 | 980101129 | 1016311397 | 1099769583 | 0 | SRX14357141 | SRS12170691 | SRA1380529 | ZMF, University Heidelberg | ZMF, University Heidelberg | 1 | 0.95873 | 0.07925 | 0.67872 | 0.47825 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2022-03-03 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||
| 68845 | 68845 | SRR18210601 | SRX14357140 | SRS12170690 | SRP362286 | PRJNA812402 | Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3 / knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3] | GSE197826 | Transcriptome Analysis | Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1 Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1 elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1 / elmo2+/+ and elmo2 / and elmo3+/+ and elmo3 / zebrafish larvae at 120 hpf Here we provide the sequencing data of elmo3+/+ and elmo3 / . Overall design: Total RNA profiles of wildtype and homozygous elmo3 knockout zebrafish larvae samples | parent bioproject:PRJNA812396 | pubmed:35874819 | elmo3+/+ wildtype rep5 | GSM5930972 | source name:30 zebrafish larvae|genotype/variation:WT|tissue:30 zebrafish larvae | elmo3+/+ wildtype rep5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | 30 zebrafish larvae | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype/variation:WT|tissue:30 zebrafish larvae | GSM5930972 | GSM5930972: elmo3+/+ wildtype rep5; Danio rerio; RNA Seq | GSM5930972 r1 | GSM5930972 | 1 | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP362286 | K38_1.fq.gz K38_2.fq.gz | fastq fastq | 4199088000.0 | 41990880.0 | GSM5930972 r1 | 0:100 1:100 | A:1096387015;C:984986485;G:1022924263;T:1094790237;N:0 | 100 | 100 | 1096387015 | 984986485 | 1022924263 | 1094790237 | 0 | SRX14357140 | SRS12170690 | SRA1380529 | ZMF, University Heidelberg | ZMF, University Heidelberg | 1 | 0.9582 | 0.07627 | 0.67951 | 0.48719 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2022-03-03 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||
| 68846 | 68846 | SRR18210602 | SRX14357139 | SRS12170688 | SRP362286 | PRJNA812402 | Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3 / knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3] | GSE197826 | Transcriptome Analysis | Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1 Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1 elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1 / elmo2+/+ and elmo2 / and elmo3+/+ and elmo3 / zebrafish larvae at 120 hpf Here we provide the sequencing data of elmo3+/+ and elmo3 / . Overall design: Total RNA profiles of wildtype and homozygous elmo3 knockout zebrafish larvae samples | parent bioproject:PRJNA812396 | pubmed:35874819 | elmo3+/+ wildtype rep4 | GSM5930971 | source name:30 zebrafish larvae|genotype/variation:WT|tissue:30 zebrafish larvae | elmo3+/+ wildtype rep4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | 30 zebrafish larvae | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype/variation:WT|tissue:30 zebrafish larvae | GSM5930971 | GSM5930971: elmo3+/+ wildtype rep4; Danio rerio; RNA Seq | GSM5930971 r1 | GSM5930971 | 1 | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP362286 | K37_1.fq.gz K37_2.fq.gz | fastq fastq | 4198821000.0 | 41988210.0 | GSM5930971 r1 | 0:100 1:100 | A:1105955288;C:977243476;G:1012685466;T:1102936770;N:0 | 100 | 100 | 1105955288 | 977243476 | 1012685466 | 1102936770 | 0 | SRX14357139 | SRS12170688 | SRA1380529 | ZMF, University Heidelberg | ZMF, University Heidelberg | 1 | 0.9565 | 0.07944 | 0.67063 | 0.47916 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2022-03-03 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||
| 68847 | 68847 | SRR18210603 | SRX14357138 | SRS12170693 | SRP362286 | PRJNA812402 | Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3 / knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3] | GSE197826 | Transcriptome Analysis | Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1 Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1 elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1 / elmo2+/+ and elmo2 / and elmo3+/+ and elmo3 / zebrafish larvae at 120 hpf Here we provide the sequencing data of elmo3+/+ and elmo3 / . Overall design: Total RNA profiles of wildtype and homozygous elmo3 knockout zebrafish larvae samples | parent bioproject:PRJNA812396 | pubmed:35874819 | elmo3+/+ wildtype rep3 | GSM5930970 | source name:30 zebrafish larvae|genotype/variation:WT|tissue:30 zebrafish larvae | elmo3+/+ wildtype rep3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | 30 zebrafish larvae | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype/variation:WT|tissue:30 zebrafish larvae | GSM5930970 | GSM5930970: elmo3+/+ wildtype rep3; Danio rerio; RNA Seq | GSM5930970 r1 | GSM5930970 | 1 | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP362286 | K36_1.fq.gz K36_2.fq.gz | fastq fastq | 4199486600.0 | 41994866.0 | GSM5930970 r1 | 0:100 1:100 | A:1114778838;C:969421442;G:1000140756;T:1115145564;N:0 | 100 | 100 | 1114778838 | 969421442 | 1000140756 | 1115145564 | 0 | SRX14357138 | SRS12170693 | SRA1380529 | ZMF, University Heidelberg | ZMF, University Heidelberg | 1 | 0.95456 | 0.09602 | 0.68406 | 0.49806 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2022-03-03 | Larval | Larval | Undetermined | Undetermined | |||||||||||||||||
| 68848 | 68848 | SRR18210604 | SRX14357137 | SRS12170689 | SRP362286 | PRJNA812402 | Transcriptome analysis of wildtype elmo3+/+ and homozygous elmo3 / knockout zebrafish larvae at 120 hpf through next generation RNA sequencing [dataset 3] | GSE197826 | Transcriptome Analysis | Elmo3 is one member of the Elmo protein family. In our study we addressed the question if the functions of Elmo1 Elmo2 and Elmo3 ware consistent or if they differ. With the CRISPR/Cas9 system we generated single knockout mutants of elmo1 elmo2 and elmo3 in the zebrafish. To assess the impact of the loss of one of the proteins on the transcriptome of a developing organism we did RNA sequencing and transcriptome analysis with elmo1+/+ and elmo1 / elmo2+/+ and elmo2 / and elmo3+/+ and elmo3 / zebrafish larvae at 120 hpf Here we provide the sequencing data of elmo3+/+ and elmo3 / . Overall design: Total RNA profiles of wildtype and homozygous elmo3 knockout zebrafish larvae samples | parent bioproject:PRJNA812396 | pubmed:35874819 | elmo3+/+ wildtype rep2 | GSM5930969 | source name:30 zebrafish larvae|genotype/variation:WT|tissue:30 zebrafish larvae | elmo3+/+ wildtype rep2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | 30 zebrafish larvae | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype/variation:WT|tissue:30 zebrafish larvae | GSM5930969 | GSM5930969: elmo3+/+ wildtype rep2; Danio rerio; RNA Seq | GSM5930969 r1 | GSM5930969 | 1 | 30 larvae per sample were snap frozen. Then total RNA was isolated using the RNeasy Kit Qiagen following the manufacturer's protocol RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP362286 | K35_1.fq.gz K35_2.fq.gz | fastq fastq | 4198805400.0 | 41988054.0 | GSM5930969 r1 | 0:100 1:100 | A:1097640425;C:986642023;G:1018581653;T:1095941299;N:0 | 100 | 100 | 1097640425 | 986642023 | 1018581653 | 1095941299 | 0 | SRX14357137 | SRS12170689 | SRA1380529 | ZMF, University Heidelberg | ZMF, University Heidelberg | 1 | 0.95929 | 0.07314 | 0.67217 | 0.49183 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2022-03-03 | Larval | Larval | Undetermined | Undetermined |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;