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run_metadata

289 rows where experiment.library_selection = "PCR", experiment.library_source = "TRANSCRIPTOMIC" and tissue_curation_coarse = "Surface Structure"

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devstage_curation 5

devstage_curation_coarse 4

tissue_curation 2

experiment.platform 2

experiment.library_strategy 2

experiment.library_layout 2

tissue_curation_coarse 1

  • Surface Structure · 289 ✖

technology 1

experiment.library_source 1

  • TRANSCRIPTOMIC · 289 ✖

experiment.library_selection 1

  • PCR · 289 ✖
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
29168 29168 SRR27217530 SRX22896259 SRS19868304 SRP478184 PRJNA1052591 Danio rerio Raw sequence reads PRJNA1052591 Other Knockout transcriptome sequencing of TRPA1b gene in zebrafish         WT PGC 24 3   strain:WT3|age:1.25dpf|collection date:2023 08 21|geo loc name:China: shanghai|sex:not determined|tissue:trunk|BioSampleModel:Model organism or animal                 WT PGC 24 3 WT PGC 24 3 WT PGC 24 3 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP478184     WT_PGC_24-3_R2.fq.gz WT_PGC_24-3_R1.fq.gz fastq fastq 6949077900.0 23163593.0 WT PGC 24 3 R1.fq.gz 0:150 1:150 A:1804348571;C:1658503849;G:1701777260;T:1784405264;N:42956 150 150     1804348571 1658503849 1701777260 1784405264 42956 SRX22896259 SRS19868304 SRA1769619 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University 2 0.95381 0.95191 0.06445 0.06402 0.7069 0.7083 0.47573 0.47795 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-12-15 Pharyngula Embryo Trunk Surface Structure
29169 29169 SRR27217531 SRX22896258 SRS19868303 SRP478184 PRJNA1052591 Danio rerio Raw sequence reads PRJNA1052591 Other Knockout transcriptome sequencing of TRPA1b gene in zebrafish         WT PGC 24 2   strain:WT2|age:1.25dpf|collection date:2023 08 21|geo loc name:China: shanghai|sex:not determined|tissue:trunk|BioSampleModel:Model organism or animal                 WT PGC 24 2 WT PGC 24 2 WT PGC 24 2 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP478184     WT_PGC_24-2_R1.fq.gz WT_PGC_24-2_R2.fq.gz fastq fastq 6675099900.0 22250333.0 WT PGC 24 2 R1.fq.gz 0:150 1:150 A:1719486221;C:1606465584;G:1644483527;T:1704624083;N:40485 150 150     1719486221 1606465584 1644483527 1704624083 40485 SRX22896258 SRS19868303 SRA1769619 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University 2 0.95744 0.95652 0.04846 0.04825 0.70804 0.70912 0.46447 0.46577 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-12-15 Pharyngula Embryo Trunk Surface Structure
29170 29170 SRR27217532 SRX22896257 SRS19868302 SRP478184 PRJNA1052591 Danio rerio Raw sequence reads PRJNA1052591 Other Knockout transcriptome sequencing of TRPA1b gene in zebrafish         WT PGC 24 1   strain:WT1|age:1.25dpf|collection date:2023 08 21|geo loc name:China: shanghai|sex:not determined|tissue:trunk|BioSampleModel:Model organism or animal                 WT PGC 24 1 WT PGC 24 1 WT PGC 24 1 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP478184     WT_PGC_24-1_R1.fq.gz WT_PGC_24-1_R2.fq.gz fastq fastq 7064831700.0 23549439.0 WT PGC 24 1 R1.fq.gz 0:150 1:150 A:1832305833;C:1686352652;G:1738278540;T:1807852822;N:41853 150 150     1832305833 1686352652 1738278540 1807852822 41853 SRX22896257 SRS19868302 SRA1769619 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University 2 0.95848 0.95777 0.0631 0.06254 0.72157 0.72247 0.4731 0.47372 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-12-15 Pharyngula Embryo Trunk Surface Structure
29171 29171 SRR27217533 SRX22896256 SRS19868301 SRP478184 PRJNA1052591 Danio rerio Raw sequence reads PRJNA1052591 Other Knockout transcriptome sequencing of TRPA1b gene in zebrafish         A1 PGC 24 3   strain:TRPA1b KO3|age:1.25dpf|collection date:2023 08 21|geo loc name:China: shanghai|sex:not determined|tissue:trunk|BioSampleModel:Model organism or animal                 A1 PGC 24 3 A1 PGC 24 3 A1 PGC 24 3 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP478184     A1_PGC_24-3_R1.fq.gz A1_PGC_24-3_R2.fq.gz fastq fastq 6953061600.0 23176872.0 A1 PGC 24 3 R1.fq.gz 0:150 1:150 A:1810976064;C:1652614300;G:1697456695;T:1791972886;N:41655 150 150     1810976064 1652614300 1697456695 1791972886 41655 SRX22896256 SRS19868301 SRA1769619 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University 2 0.95143 0.95105 0.07009 0.06986 0.69627 0.6969 0.46658 0.46554 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-12-15 Pharyngula Embryo Trunk Surface Structure
29172 29172 SRR27217534 SRX22896255 SRS19868300 SRP478184 PRJNA1052591 Danio rerio Raw sequence reads PRJNA1052591 Other Knockout transcriptome sequencing of TRPA1b gene in zebrafish         A1 PGC 24 2   strain:TRPA1b KO2|age:1.25dpf|collection date:2023 08 21|geo loc name:China: shanghai|sex:not determined|tissue:trunk|BioSampleModel:Model organism or animal                 A1 PGC 24 2 A1 PGC 24 2 A1 PGC 24 2 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP478184     A1_PGC_24-2_R1.fq.gz A1_PGC_24-2_R2.fq.gz fastq fastq 6940389600.0 23134632.0 A1 PGC 24 2 R1.fq.gz 0:150 1:150 A:1785833122;C:1673393460;G:1710182746;T:1770937783;N:42489 150 150     1785833122 1673393460 1710182746 1770937783 42489 SRX22896255 SRS19868300 SRA1769619 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University 2 0.95372 0.95441 0.06919 0.06949 0.70013 0.70177 0.47547 0.47456 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-12-15 Pharyngula Embryo Trunk Surface Structure
29173 29173 SRR27217535 SRX22896254 SRS19868299 SRP478184 PRJNA1052591 Danio rerio Raw sequence reads PRJNA1052591 Other Knockout transcriptome sequencing of TRPA1b gene in zebrafish         A1 PGC 24 1   strain:TRPA1b KO1|age:1.25dpf|collection date:2023 08 21|geo loc name:China: shanghai|sex:not determined|tissue:trunk|BioSampleModel:Model organism or animal                 A1 PGC 24 1 A1 PGC 24 1 A1 PGC 24 1 ribonucleic acid     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP478184     A1_PGC_24-1_R1.fq.gz A1_PGC_24-1_R2.fq.gz fastq fastq 6604300500.0 22014335.0 A1 PGC 24 1 R1.fq.gz 0:150 1:150 A:1719784265;C:1571368991;G:1612164427;T:1700943908;N:38909 150 150     1719784265 1571368991 1612164427 1700943908 38909 SRX22896254 SRS19868299 SRA1769619 Shanghai Ocean University|College of Aquaculture and Life Sciences Shanghai Ocean University 2 0.95474 0.95309 0.06766 0.06685 0.69753 0.69929 0.47173 0.46856 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2023-12-15 Pharyngula Embryo Trunk Surface Structure
30702 30702 SRR28328136 SRX23936571 SRS20740255 SRP494948 PRJNA1086823 Danio rerio Raw sequence reads PRJNA1086823 Whole Genome Sequencing Study the effects on the body when this gene is lost     Study the effects on the body when this gene is lost Model organism or animal sample from Danio rerio tu   strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:missing|BioSampleModel:Model organism or animal                 SampleF 6 6 control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP494948     tu_3.R1.raw.fastq.gz tu_3.R2.raw.fastq.gz fastq fastq 6836795894.0 22638397.0 tu 3.R1.raw.fastq.gz 0:151 1:151 A:1911756035;C:1496221872;G:1563235044;T:1865509810;N:73133 151 151     1911756035 1496221872 1563235044 1865509810 73133 SRX23936571 SRS20740255 SRA1823374 Hunan Normal University|Hunan Normal University Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-13 Undetermined Undetermined Trunk Surface Structure
30703 30703 SRR28328137 SRX23936570 SRS20740255 SRP494948 PRJNA1086823 Danio rerio Raw sequence reads PRJNA1086823 Whole Genome Sequencing Study the effects on the body when this gene is lost     Study the effects on the body when this gene is lost Model organism or animal sample from Danio rerio tu   strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:missing|BioSampleModel:Model organism or animal                 SampleE 5 5 control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP494948     tu_2.R1.raw.fastq.gz tu_2.R2.raw.fastq.gz fastq fastq 6933313282.0 22957991.0 tu 2.R1.raw.fastq.gz 0:151 1:151 A:1895897966;C:1562896362;G:1633152399;T:1841286721;N:79834 151 151     1895897966 1562896362 1633152399 1841286721 79834 SRX23936570 SRS20740255 SRA1823374 Hunan Normal University|Hunan Normal University Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-13 Undetermined Undetermined Trunk Surface Structure
30704 30704 SRR28328138 SRX23936569 SRS20740255 SRP494948 PRJNA1086823 Danio rerio Raw sequence reads PRJNA1086823 Whole Genome Sequencing Study the effects on the body when this gene is lost     Study the effects on the body when this gene is lost Model organism or animal sample from Danio rerio tu   strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|biomaterial provider:missing|BioSampleModel:Model organism or animal                 SampleD 4 4 control     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP494948     tu_1.R1.raw.fastq.gz tu_1.R2.raw.fastq.gz fastq fastq 6953463930.0 23024715.0 tu 1.R1.raw.fastq.gz 0:151 1:151 A:1914281996;C:1558685345;G:1630355775;T:1850061551;N:79263 151 151     1914281996 1558685345 1630355775 1850061551 79263 SRX23936569 SRS20740255 SRA1823374 Hunan Normal University|Hunan Normal University Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-13 Undetermined Undetermined Trunk Surface Structure
30705 30705 SRR28328139 SRX23936568 SRS20740254 SRP494948 PRJNA1086823 Danio rerio Raw sequence reads PRJNA1086823 Whole Genome Sequencing Study the effects on the body when this gene is lost     Study the effects on the body when this gene is lost Model organism or animal sample from Danio rerio myo7aa   strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|BioSampleModel:Model organism or animal                 SampleC 3 3 treatment     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP494948     myo7aa_3.R1.raw.fastq.gz myo7aa_3.R2.raw.fastq.gz fastq fastq 6793366180.0 22494590.0 myo7aa 3.R1.raw.fastq.gz 0:151 1:151 A:1786353133;C:1602317410;G:1674855786;T:1729822151;N:17700 151 151     1786353133 1602317410 1674855786 1729822151 17700 SRX23936568 SRS20740254 SRA1823374 Hunan Normal University|Hunan Normal University Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-13 Undetermined Undetermined Trunk Surface Structure
30706 30706 SRR28328140 SRX23936567 SRS20740254 SRP494948 PRJNA1086823 Danio rerio Raw sequence reads PRJNA1086823 Whole Genome Sequencing Study the effects on the body when this gene is lost     Study the effects on the body when this gene is lost Model organism or animal sample from Danio rerio myo7aa   strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|BioSampleModel:Model organism or animal                 SampleB 2 2 treatment     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP494948     myo7aa_2.R1.raw.fastq.gz myo7aa_2.R2.raw.fastq.gz fastq fastq 6762797438.0 22393369.0 myo7aa 2.R1.raw.fastq.gz 0:151 1:151 A:1816704062;C:1557768239;G:1627373716;T:1760926609;N:24812 151 151     1816704062 1557768239 1627373716 1760926609 24812 SRX23936567 SRS20740254 SRA1823374 Hunan Normal University|Hunan Normal University Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-13 Undetermined Undetermined Trunk Surface Structure
30707 30707 SRR28328141 SRX23936566 SRS20740254 SRP494948 PRJNA1086823 Danio rerio Raw sequence reads PRJNA1086823 Whole Genome Sequencing Study the effects on the body when this gene is lost     Study the effects on the body when this gene is lost Model organism or animal sample from Danio rerio myo7aa   strain:FISH|age:2|collection date:2023 02 28|geo loc name:missing|sex:missing|tissue:missing|BioSampleModel:Model organism or animal                 SampleA 1 1 treatment     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP494948     myo7aa_1.R1.raw.fastq.gz myo7aa_1.R2.raw.fastq.gz fastq fastq 6605710628.0 21873214.0 myo7aa 1.R1.raw.fastq.gz 0:151 1:151 A:1728796843;C:1565920605;G:1629477870;T:1681497978;N:17332 151 151     1728796843 1565920605 1629477870 1681497978 17332 SRX23936566 SRS20740254 SRA1823374 Hunan Normal University|Hunan Normal University Hunan Normal University                       B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-13 Undetermined Undetermined Trunk Surface Structure
31530 31530 SRR28467112 SRX24070103 SRS20860625 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         BPM 1   strain:AB Wild type|isolate:Zebrafish of BPM treatment group 1|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY BPM 1 ZXY BPM 1 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     BPM1.raw_2.fastq.gz BPM1.raw_1.fastq.gz fastq fastq 9394450800.0 31314836.0 BPM1.raw 1.fastq.gz 0:150 1:150 A:2554382711;C:2098883579;G:2207645797;T:2533462469;N:76244 150 150     2554382711 2098883579 2207645797 2533462469 76244 SRX24070103 SRS20860625 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.94127 0.93972 0.1164 0.11723 0.67308 0.67673 0.49857 0.50613 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31531 31531 SRR28467113 SRX24070102 SRS20860624 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         BPG 3   strain:AB Wild type|isolate:Zebrafish of BPG treatment group 3|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY BPG 3 ZXY BPG 3 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     BPG3.raw_1.fastq.gz BPG3.raw_2.fastq.gz fastq fastq 10077237000.0 33590790.0 BPG3.raw 1.fastq.gz 0:150 1:150 A:2739033278;C:2249842624;G:2379133275;T:2709150044;N:77779 150 150     2739033278 2249842624 2379133275 2709150044 77779 SRX24070102 SRS20860624 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.94306 0.94056 0.10748 0.10702 0.67653 0.67986 0.5156 0.50914 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31532 31532 SRR28467114 SRX24070101 SRS20860623 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         BPG 2   strain:AB Wild type|isolate:Zebrafish of BPG treatment group 2|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY BPG 2 ZXY BPG 2 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     BPG2.raw_2.fastq.gz BPG2.raw_1.fastq.gz fastq fastq 9510942300.0 31703141.0 BPG2.raw 1.fastq.gz 0:150 1:150 A:2596352503;C:2120752906;G:2233383807;T:2560375232;N:77852 150 150     2596352503 2120752906 2233383807 2560375232 77852 SRX24070101 SRS20860623 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.94667 0.94269 0.10626 0.10688 0.67533 0.68081 0.49483 0.49423 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31533 31533 SRR28467115 SRX24070100 SRS20860622 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         BPG 1   strain:AB Wild type|isolate:Zebrafish of BPG treatment group 1|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY BPG 1 ZXY BPG 1 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     BPG1.raw_1.fastq.gz BPG1.raw_2.fastq.gz fastq fastq 13070106300.0 43567021.0 BPG1.raw 1.fastq.gz 0:150 1:150 A:3534452437;C:2939996996;G:3085563305;T:3509989820;N:103742 150 150     3534452437 2939996996 3085563305 3509989820 103742 SRX24070100 SRS20860622 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.9438 0.94084 0.10523 0.10522 0.67829 0.68073 0.49381 0.49067 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31534 31534 SRR28467116 SRX24070099 SRS20860621 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         BPA 3   strain:AB Wild type|isolate:Zebrafish of BPA treatment group 3|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY BPA 3 ZXY BPA 3 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     BPA3.raw_2.fastq.gz BPA3.raw_1.fastq.gz fastq fastq 10411684500.0 34705615.0 BPA3.raw 1.fastq.gz 0:150 1:150 A:2832043862;C:2321319365;G:2455663475;T:2802571018;N:86780 150 150     2832043862 2321319365 2455663475 2802571018 86780 SRX24070099 SRS20860621 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.94457 0.94104 0.11054 0.10975 0.66994 0.67318 0.51406 0.50942 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31535 31535 SRR28467117 SRX24070098 SRS20860620 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         BPA 2   strain:AB Wild type|isolate:Zebrafish of BPA treatment group 2|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY BPA 2 ZXY BPA 2 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     BPA2.raw_1.fastq.gz BPA2.raw_2.fastq.gz fastq fastq 9661415100.0 32204717.0 BPA2.raw 1.fastq.gz 0:150 1:150 A:2627401085;C:2157294589;G:2278953763;T:2597686452;N:79211 150 150     2627401085 2157294589 2278953763 2597686452 79211 SRX24070098 SRS20860620 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.9432 0.94024 0.10905 0.10878 0.67304 0.6775 0.50281 0.50407 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31536 31536 SRR28467118 SRX24070097 SRS20860619 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         BPA 1   strain:AB Wild type|isolate:Zebrafish of BPA treatment group 1|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY BPA 1 ZXY BPA 1 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     BPA1.raw_1.fastq.gz BPA1.raw_2.fastq.gz fastq fastq 9717716400.0 32392388.0 BPA1.raw 1.fastq.gz 0:150 1:150 A:2650893145;C:2181496527;G:2254888972;T:2630357805;N:79951 150 150     2650893145 2181496527 2254888972 2630357805 79951 SRX24070097 SRS20860619 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.94789 0.94422 0.10681 0.1065 0.66833 0.67377 0.50841 0.5025 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31537 31537 SRR28467119 SRX24070096 SRS20860618 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         Control 3   strain:AB Wild type|isolate:Zebrafish of blank control group 3|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY CK 3 ZXY CK 3 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     Control3.raw_1.fastq.gz Control3.raw_2.fastq.gz fastq fastq 8827093200.0 29423644.0 Control3.raw 1.fastq.gz 0:150 1:150 A:2394211757;C:1989274047;G:2061489648;T:2382044834;N:72914 150 150     2394211757 1989274047 2061489648 2382044834 72914 SRX24070096 SRS20860618 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.94786 0.9448 0.10432 0.10422 0.67221 0.67383 0.51187 0.50251 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31538 31538 SRR28467120 SRX24070095 SRS20860617 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         BPTMC 3   strain:AB Wild type|isolate:Zebrafish of BPTMC treatment group 3|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY BPTMC 3 ZXY BPTMC 3 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     BPTMC3.raw_1.fastq.gz BPTMC3.raw_2.fastq.gz fastq fastq 10073599500.0 33578665.0 BPTMC3.raw 1.fastq.gz 0:150 1:150 A:2703808743;C:2256806609;G:2438554304;T:2674346802;N:83042 150 150     2703808743 2256806609 2438554304 2674346802 83042 SRX24070095 SRS20860617 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.94379 0.89251 0.09996 0.09437 0.67961 0.68976 0.50126 0.51462 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31539 31539 SRR28467121 SRX24070094 SRS20860616 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         BPTMC 2   strain:AB Wild type|isolate:Zebrafish of BPTMC treatment group 2|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY BPTMC 2 ZXY BPTMC 2 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     BPTMC2.raw_1.fastq.gz BPTMC2.raw_2.fastq.gz fastq fastq 9429771000.0 31432570.0 BPTMC2.raw 1.fastq.gz 0:150 1:150 A:2563993022;C:2099927909;G:2215282718;T:2550488919;N:78432 150 150     2563993022 2099927909 2215282718 2550488919 78432 SRX24070094 SRS20860616 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.94015 0.93845 0.11202 0.11225 0.68142 0.68426 0.50947 0.46648 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31540 31540 SRR28467122 SRX24070093 SRS20860615 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         BPTMC 1   strain:AB Wild type|isolate:Zebrafish of BPTMC treatment group 1|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY BPTMC 1 ZXY BPTMC 1 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     BPTMC1.raw_1.fastq.gz BPTMC1.raw_2.fastq.gz fastq fastq 10306275300.0 34354251.0 BPTMC1.raw 1.fastq.gz 0:150 1:150 A:2813926642;C:2292771191;G:2419432993;T:2780059784;N:84690 150 150     2813926642 2292771191 2419432993 2780059784 84690 SRX24070093 SRS20860615 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.9416 0.93867 0.11422 0.11418 0.68018 0.6856 0.48529 0.48762 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31541 31541 SRR28467123 SRX24070092 SRS20860614 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         BPM 3   strain:AB Wild type|isolate:Zebrafish of BPM treatment group 3|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY BPM 3 ZXY BPM 3 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     BPM3.raw_1.fastq.gz BPM3.raw_2.fastq.gz fastq fastq 9935041500.0 33116805.0 BPM3.raw 1.fastq.gz 0:150 1:150 A:2699556183;C:2237493304;G:2314599682;T:2683312551;N:79780 150 150     2699556183 2237493304 2314599682 2683312551 79780 SRX24070092 SRS20860614 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.94795 0.94397 0.10579 0.10508 0.67304 0.67614 0.48977 0.49037 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31542 31542 SRR28467124 SRX24070091 SRS20860613 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         BPM 2   strain:AB Wild type|isolate:Zebrafish of BPM treatment group 2|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY BPM 2 ZXY BPM 2 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     BPM2.raw_1.fastq.gz BPM2.raw_2.fastq.gz fastq fastq 8645715900.0 28819053.0 BPM2.raw 1.fastq.gz 0:150 1:150 A:2370941492;C:1921770882;G:2002106055;T:2350824859;N:72612 150 150     2370941492 1921770882 2002106055 2350824859 72612 SRX24070091 SRS20860613 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.94303 0.93986 0.1216 0.12095 0.67154 0.67385 0.4964 0.49763 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31543 31543 SRR28467125 SRX24070090 SRS20860612 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         Control 2   strain:AB Wild type|isolate:Zebrafish of blank control group 2|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY CK 2 ZXY CK 2 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     Control2.raw_1.fastq.gz Control2.raw_2.fastq.gz fastq fastq 8728743900.0 29095813.0 Control2.raw 1.fastq.gz 0:150 1:150 A:2347809691;C:1937189854;G:2127437851;T:2316234453;N:72051 150 150     2347809691 1937189854 2127437851 2316234453 72051 SRX24070090 SRS20860612 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.94052 0.93739 0.10645 0.10488 0.67915 0.68377 0.51064 0.50924 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
31544 31544 SRR28467126 SRX24070089 SRS20860611 SRP498043 PRJNA1091388 Danio rerio Raw sequence reads PRJNA1091388 Whole Genome Sequencing normal RNA seq of Danio rerio         Control 1   strain:AB Wild type|isolate:Zebrafish of blank control group 1|breed:no collected|cultivar:no collected|ecotype:Nanjing|age:5 dpf stage:larval fish|collection date:2023 02|geo loc name:China: Nanjing|sex:not applicable|tissue:the whole body|BioSampleModel:Model organism or animal                 RNA Seq of Zebrafish larvae ZXY CK 1 ZXY CK 1 Total RNA was isolated and purified from zebrafish roe tissues using TRIzol reagent.RNA quantity and purity were quantified using an ultra micro spectrophotometer and agarose gel electrophoresis was used to avoid alteration of RNA integrity and purity. RNA and DNA were quantified using the Qubit 2.0 RNA and Qubit 2.0 DNA kits. Subsequently the extracted RNA was transformed to construct cDNA sequencing libraries using the TrueLib mRNA Library Prep Kit for Illumina. post quantification and pooling of cDNA using AgilentBioAnalyzer 2100 sequencing was performed on NovaSeq 6000. The quality of sequencing data was assessed and low quality sequences were filtered by FastQC 0.11.9 and Trimmomatic 0.32. Filtered sequenced sequences were aligned with the zebrafish reference genome using HiSAT2 2.2.1 and finally transcripts were analyzed for gene expression levels by StringTie software     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP498043     Control1.raw_1.fastq.gz Control1.raw_2.fastq.gz fastq fastq 13197587400.0 43991958.0 Control1.raw 1.fastq.gz 0:150 1:150 A:3499966481;C:3072967049;G:3152583762;T:3471963983;N:106125 150 150     3499966481 3072967049 3152583762 3471963983 106125 SRX24070089 SRS20860611 SRA1834298 Chinese Academy of Agricultural Sciences|Institute of Quality Standards and Testing Technol Chinese Academy of Agricultural Sciences 2 0.9548 0.95216 0.08791 0.08792 0.66841 0.67241 0.48738 0.48068 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2024-03-27 Larval Larval Trunk Surface Structure
34605 34605 SRR32129951 SRX27476252 SRS23900301 SRP559953 PRJNA1215813 Comparative Toxicological Effects of Tire Wear and Latex Particle Leachates in Zebrafish Embryos: Focus on Oxidative Stress and Ferroptosis PRJNA1215813 Other Microrubber a subset of microplastics has emerged as a significant environmental concern due to its persistence bioaccumulation and potential toxicity in aquatic ecosystems. This study investigates the toxicological effects of leachates derived from tire wear particles TWP and latex particles LAP on zebrafish embryos focusing on physiological oxidative stress and transcriptomic responses. LAP leachate exhibited significantly higher toxicity than TWP characterized by increased mortality delayed hatching reduced spontaneous movement suppressed heart rate and severe morphological malformations. Chemical analysis identified elevated levels of heavy metals and biologically active organic compounds with higher zinc concentrations and benzothiazole derivatives in LAP leachate contributing to its greater toxicity. Oxidative stress markers revealed elevated catalase CAT and malondialdehyde MDA levels in both groups but LAP exposure significantly reduced glutathione S transferase GST activity indicating compromised detoxification capacity. Transcriptomic analysis identified ferroptosis as a central pathway mediating toxicity in both leachates. LAP exposure was associated with the upregulation of mt2 and fthl31 and the downregulation of slc40a1 suggesting disrupted iron metabolism and exacerbated oxidative damage. In contrast TWP exposure triggered adaptive responses including the upregulation of detoxification related genes such as cyp1a and gstt1b. These findings elucidate distinct toxicity mechanisms between TWP and LAP leachates and underscore the need for enhanced environmental monitoring and regulatory strategies to mitigate their ecological impacts.         LAP3   breed:AB|age:5 days|collection date:2024 05 26|geo loc name:Not collected|sex:Missing|tissue:Whole body|Replicate:Replicate = biological replicate 9|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: zebrafish embryos LAP3 LAP3 mRNA seq of Danio rerio relication 3 of LAP     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP559953     SLAP3.R1.raw.fastq.gz SLAP3.R2.raw.fastq.gz fastq fastq 7183254522.0 23785611.0 SLAP3.R1.raw.fastq.gz 0:151 1:151 A:1882819072;C:1681966830;G:1744461184;T:1873823146;N:184290 151 151     1882819072 1681966830 1744461184 1873823146 184290 SRX27476252 SRS23900301 SRA2060932 Qingdao University of Science and Technology|College of Marine Science and biological engineeri Qingdao University of Science and Technology                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-26 Larval Larval Trunk Surface Structure
34606 34606 SRR32129952 SRX27476251 SRS23900300 SRP559953 PRJNA1215813 Comparative Toxicological Effects of Tire Wear and Latex Particle Leachates in Zebrafish Embryos: Focus on Oxidative Stress and Ferroptosis PRJNA1215813 Other Microrubber a subset of microplastics has emerged as a significant environmental concern due to its persistence bioaccumulation and potential toxicity in aquatic ecosystems. This study investigates the toxicological effects of leachates derived from tire wear particles TWP and latex particles LAP on zebrafish embryos focusing on physiological oxidative stress and transcriptomic responses. LAP leachate exhibited significantly higher toxicity than TWP characterized by increased mortality delayed hatching reduced spontaneous movement suppressed heart rate and severe morphological malformations. Chemical analysis identified elevated levels of heavy metals and biologically active organic compounds with higher zinc concentrations and benzothiazole derivatives in LAP leachate contributing to its greater toxicity. Oxidative stress markers revealed elevated catalase CAT and malondialdehyde MDA levels in both groups but LAP exposure significantly reduced glutathione S transferase GST activity indicating compromised detoxification capacity. Transcriptomic analysis identified ferroptosis as a central pathway mediating toxicity in both leachates. LAP exposure was associated with the upregulation of mt2 and fthl31 and the downregulation of slc40a1 suggesting disrupted iron metabolism and exacerbated oxidative damage. In contrast TWP exposure triggered adaptive responses including the upregulation of detoxification related genes such as cyp1a and gstt1b. These findings elucidate distinct toxicity mechanisms between TWP and LAP leachates and underscore the need for enhanced environmental monitoring and regulatory strategies to mitigate their ecological impacts.         LAP2   breed:AB|age:5 days|collection date:2024 05 26|geo loc name:Not collected|sex:Missing|tissue:Whole body|Replicate:Replicate = biological replicate 8|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: zebrafish embryos LAP2 LAP2 mRNA seq of Danio rerio relication 2 of LAP     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP559953     SLAP2.R1.raw.fastq.gz SLAP2.R2.raw.fastq.gz fastq fastq 7139867692.0 23641946.0 SLAP2.R1.raw.fastq.gz 0:151 1:151 A:1904886971;C:1644487548;G:1698548524;T:1891760900;N:183749 151 151     1904886971 1644487548 1698548524 1891760900 183749 SRX27476251 SRS23900300 SRA2060932 Qingdao University of Science and Technology|College of Marine Science and biological engineeri Qingdao University of Science and Technology                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-26 Larval Larval Trunk Surface Structure
34607 34607 SRR32129953 SRX27476250 SRS23900299 SRP559953 PRJNA1215813 Comparative Toxicological Effects of Tire Wear and Latex Particle Leachates in Zebrafish Embryos: Focus on Oxidative Stress and Ferroptosis PRJNA1215813 Other Microrubber a subset of microplastics has emerged as a significant environmental concern due to its persistence bioaccumulation and potential toxicity in aquatic ecosystems. This study investigates the toxicological effects of leachates derived from tire wear particles TWP and latex particles LAP on zebrafish embryos focusing on physiological oxidative stress and transcriptomic responses. LAP leachate exhibited significantly higher toxicity than TWP characterized by increased mortality delayed hatching reduced spontaneous movement suppressed heart rate and severe morphological malformations. Chemical analysis identified elevated levels of heavy metals and biologically active organic compounds with higher zinc concentrations and benzothiazole derivatives in LAP leachate contributing to its greater toxicity. Oxidative stress markers revealed elevated catalase CAT and malondialdehyde MDA levels in both groups but LAP exposure significantly reduced glutathione S transferase GST activity indicating compromised detoxification capacity. Transcriptomic analysis identified ferroptosis as a central pathway mediating toxicity in both leachates. LAP exposure was associated with the upregulation of mt2 and fthl31 and the downregulation of slc40a1 suggesting disrupted iron metabolism and exacerbated oxidative damage. In contrast TWP exposure triggered adaptive responses including the upregulation of detoxification related genes such as cyp1a and gstt1b. These findings elucidate distinct toxicity mechanisms between TWP and LAP leachates and underscore the need for enhanced environmental monitoring and regulatory strategies to mitigate their ecological impacts.         LAP1   breed:AB|age:5 days|collection date:2024 05 26|geo loc name:Not collected|sex:Missing|tissue:Whole body|Replicate:Replicate = biological replicate 7|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: zebrafish embryos LAP1 LAP1 mRNA seq of Danio rerio relication 1 of LAP     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP559953     SLAP1.R1.raw.fastq.gz SLAP1.R2.raw.fastq.gz fastq fastq 7645904026.0 25317563.0 SLAP1.R1.raw.fastq.gz 0:151 1:151 A:2049503194;C:1744624826;G:1812871140;T:2038707095;N:197771 151 151     2049503194 1744624826 1812871140 2038707095 197771 SRX27476250 SRS23900299 SRA2060932 Qingdao University of Science and Technology|College of Marine Science and biological engineeri Qingdao University of Science and Technology                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-26 Larval Larval Trunk Surface Structure
34608 34608 SRR32129954 SRX27476249 SRS23900298 SRP559953 PRJNA1215813 Comparative Toxicological Effects of Tire Wear and Latex Particle Leachates in Zebrafish Embryos: Focus on Oxidative Stress and Ferroptosis PRJNA1215813 Other Microrubber a subset of microplastics has emerged as a significant environmental concern due to its persistence bioaccumulation and potential toxicity in aquatic ecosystems. This study investigates the toxicological effects of leachates derived from tire wear particles TWP and latex particles LAP on zebrafish embryos focusing on physiological oxidative stress and transcriptomic responses. LAP leachate exhibited significantly higher toxicity than TWP characterized by increased mortality delayed hatching reduced spontaneous movement suppressed heart rate and severe morphological malformations. Chemical analysis identified elevated levels of heavy metals and biologically active organic compounds with higher zinc concentrations and benzothiazole derivatives in LAP leachate contributing to its greater toxicity. Oxidative stress markers revealed elevated catalase CAT and malondialdehyde MDA levels in both groups but LAP exposure significantly reduced glutathione S transferase GST activity indicating compromised detoxification capacity. Transcriptomic analysis identified ferroptosis as a central pathway mediating toxicity in both leachates. LAP exposure was associated with the upregulation of mt2 and fthl31 and the downregulation of slc40a1 suggesting disrupted iron metabolism and exacerbated oxidative damage. In contrast TWP exposure triggered adaptive responses including the upregulation of detoxification related genes such as cyp1a and gstt1b. These findings elucidate distinct toxicity mechanisms between TWP and LAP leachates and underscore the need for enhanced environmental monitoring and regulatory strategies to mitigate their ecological impacts.         TWP3   breed:AB|age:5 days|collection date:2024 05 26|geo loc name:Not collected|sex:Missing|tissue:Whole body|Replicate:Replicate = biological replicate 6|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: zebrafish embryos TWP3 TWP3 mRNA seq of Danio rerio relication 3 of TWP     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP559953     STWP3.R1.raw.fastq.gz STWP3.R2.raw.fastq.gz fastq fastq 8096479268.0 26809534.0 STWP3.R1.raw.fastq.gz 0:151 1:151 A:2110740470;C:1903775486;G:1969223430;T:2112536317;N:203565 151 151     2110740470 1903775486 1969223430 2112536317 203565 SRX27476249 SRS23900298 SRA2060932 Qingdao University of Science and Technology|College of Marine Science and biological engineeri Qingdao University of Science and Technology                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-26 Larval Larval Trunk Surface Structure
34609 34609 SRR32129955 SRX27476248 SRS23900297 SRP559953 PRJNA1215813 Comparative Toxicological Effects of Tire Wear and Latex Particle Leachates in Zebrafish Embryos: Focus on Oxidative Stress and Ferroptosis PRJNA1215813 Other Microrubber a subset of microplastics has emerged as a significant environmental concern due to its persistence bioaccumulation and potential toxicity in aquatic ecosystems. This study investigates the toxicological effects of leachates derived from tire wear particles TWP and latex particles LAP on zebrafish embryos focusing on physiological oxidative stress and transcriptomic responses. LAP leachate exhibited significantly higher toxicity than TWP characterized by increased mortality delayed hatching reduced spontaneous movement suppressed heart rate and severe morphological malformations. Chemical analysis identified elevated levels of heavy metals and biologically active organic compounds with higher zinc concentrations and benzothiazole derivatives in LAP leachate contributing to its greater toxicity. Oxidative stress markers revealed elevated catalase CAT and malondialdehyde MDA levels in both groups but LAP exposure significantly reduced glutathione S transferase GST activity indicating compromised detoxification capacity. Transcriptomic analysis identified ferroptosis as a central pathway mediating toxicity in both leachates. LAP exposure was associated with the upregulation of mt2 and fthl31 and the downregulation of slc40a1 suggesting disrupted iron metabolism and exacerbated oxidative damage. In contrast TWP exposure triggered adaptive responses including the upregulation of detoxification related genes such as cyp1a and gstt1b. These findings elucidate distinct toxicity mechanisms between TWP and LAP leachates and underscore the need for enhanced environmental monitoring and regulatory strategies to mitigate their ecological impacts.         TWP2   breed:AB|age:5 days|collection date:2024 05 26|geo loc name:Not collected|sex:Missing|tissue:Whole body|Replicate:Replicate = biological replicate 5|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: zebrafish embryos TWP2 TWP2 mRNA seq of Danio rerio relication 2 of TWP     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP559953     STWP2.R1.raw.fastq.gz STWP2.R2.raw.fastq.gz fastq fastq 6881487968.0 22786384.0 STWP2.R1.raw.fastq.gz 0:151 1:151 A:1769568137;C:1637920699;G:1700276394;T:1773546973;N:175765 151 151     1769568137 1637920699 1700276394 1773546973 175765 SRX27476248 SRS23900297 SRA2060932 Qingdao University of Science and Technology|College of Marine Science and biological engineeri Qingdao University of Science and Technology                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-26 Larval Larval Trunk Surface Structure
34610 34610 SRR32129956 SRX27476247 SRS23900296 SRP559953 PRJNA1215813 Comparative Toxicological Effects of Tire Wear and Latex Particle Leachates in Zebrafish Embryos: Focus on Oxidative Stress and Ferroptosis PRJNA1215813 Other Microrubber a subset of microplastics has emerged as a significant environmental concern due to its persistence bioaccumulation and potential toxicity in aquatic ecosystems. This study investigates the toxicological effects of leachates derived from tire wear particles TWP and latex particles LAP on zebrafish embryos focusing on physiological oxidative stress and transcriptomic responses. LAP leachate exhibited significantly higher toxicity than TWP characterized by increased mortality delayed hatching reduced spontaneous movement suppressed heart rate and severe morphological malformations. Chemical analysis identified elevated levels of heavy metals and biologically active organic compounds with higher zinc concentrations and benzothiazole derivatives in LAP leachate contributing to its greater toxicity. Oxidative stress markers revealed elevated catalase CAT and malondialdehyde MDA levels in both groups but LAP exposure significantly reduced glutathione S transferase GST activity indicating compromised detoxification capacity. Transcriptomic analysis identified ferroptosis as a central pathway mediating toxicity in both leachates. LAP exposure was associated with the upregulation of mt2 and fthl31 and the downregulation of slc40a1 suggesting disrupted iron metabolism and exacerbated oxidative damage. In contrast TWP exposure triggered adaptive responses including the upregulation of detoxification related genes such as cyp1a and gstt1b. These findings elucidate distinct toxicity mechanisms between TWP and LAP leachates and underscore the need for enhanced environmental monitoring and regulatory strategies to mitigate their ecological impacts.         TWP1   breed:AB|age:5 days|collection date:2024 05 26|geo loc name:Not collected|sex:Missing|tissue:Whole body|Replicate:Replicate = biological replicate 4|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: zebrafish embryos TWP1 TWP1 mRNA seq of Danio rerio relication 1 of TWP     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP559953     STWP1.R1.raw.fastq.gz STWP1.R2.raw.fastq.gz fastq fastq 8138908456.0 26950028.0 STWP1.R1.raw.fastq.gz 0:151 1:151 A:2098817113;C:1934858897;G:2002571746;T:2102461754;N:198946 151 151     2098817113 1934858897 2002571746 2102461754 198946 SRX27476247 SRS23900296 SRA2060932 Qingdao University of Science and Technology|College of Marine Science and biological engineeri Qingdao University of Science and Technology                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-26 Larval Larval Trunk Surface Structure
34611 34611 SRR32129957 SRX27476246 SRS23900295 SRP559953 PRJNA1215813 Comparative Toxicological Effects of Tire Wear and Latex Particle Leachates in Zebrafish Embryos: Focus on Oxidative Stress and Ferroptosis PRJNA1215813 Other Microrubber a subset of microplastics has emerged as a significant environmental concern due to its persistence bioaccumulation and potential toxicity in aquatic ecosystems. This study investigates the toxicological effects of leachates derived from tire wear particles TWP and latex particles LAP on zebrafish embryos focusing on physiological oxidative stress and transcriptomic responses. LAP leachate exhibited significantly higher toxicity than TWP characterized by increased mortality delayed hatching reduced spontaneous movement suppressed heart rate and severe morphological malformations. Chemical analysis identified elevated levels of heavy metals and biologically active organic compounds with higher zinc concentrations and benzothiazole derivatives in LAP leachate contributing to its greater toxicity. Oxidative stress markers revealed elevated catalase CAT and malondialdehyde MDA levels in both groups but LAP exposure significantly reduced glutathione S transferase GST activity indicating compromised detoxification capacity. Transcriptomic analysis identified ferroptosis as a central pathway mediating toxicity in both leachates. LAP exposure was associated with the upregulation of mt2 and fthl31 and the downregulation of slc40a1 suggesting disrupted iron metabolism and exacerbated oxidative damage. In contrast TWP exposure triggered adaptive responses including the upregulation of detoxification related genes such as cyp1a and gstt1b. These findings elucidate distinct toxicity mechanisms between TWP and LAP leachates and underscore the need for enhanced environmental monitoring and regulatory strategies to mitigate their ecological impacts.         CONTROL3   breed:AB|age:5 days|collection date:2024 05 26|geo loc name:Not collected|sex:Missing|tissue:Whole body|Replicate:Replicate = biological replicate 3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: zebrafish embryos CONTROL3 CONTROL3 mRNA seq of Danio rerio relication 3 of CONTROL     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP559953     CONTROL3.R1.raw.fastq.gz CONTROL3.R2.raw.fastq.gz fastq fastq 7576728510.0 25088505.0 CONTROL3.R1.raw.fastq.gz 0:151 1:151 A:1944933324;C:1805382406;G:1877636209;T:1948585527;N:191044 151 151     1944933324 1805382406 1877636209 1948585527 191044 SRX27476246 SRS23900295 SRA2060932 Qingdao University of Science and Technology|College of Marine Science and biological engineeri Qingdao University of Science and Technology                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-26 Larval Larval Trunk Surface Structure
34612 34612 SRR32129958 SRX27476245 SRS23900294 SRP559953 PRJNA1215813 Comparative Toxicological Effects of Tire Wear and Latex Particle Leachates in Zebrafish Embryos: Focus on Oxidative Stress and Ferroptosis PRJNA1215813 Other Microrubber a subset of microplastics has emerged as a significant environmental concern due to its persistence bioaccumulation and potential toxicity in aquatic ecosystems. This study investigates the toxicological effects of leachates derived from tire wear particles TWP and latex particles LAP on zebrafish embryos focusing on physiological oxidative stress and transcriptomic responses. LAP leachate exhibited significantly higher toxicity than TWP characterized by increased mortality delayed hatching reduced spontaneous movement suppressed heart rate and severe morphological malformations. Chemical analysis identified elevated levels of heavy metals and biologically active organic compounds with higher zinc concentrations and benzothiazole derivatives in LAP leachate contributing to its greater toxicity. Oxidative stress markers revealed elevated catalase CAT and malondialdehyde MDA levels in both groups but LAP exposure significantly reduced glutathione S transferase GST activity indicating compromised detoxification capacity. Transcriptomic analysis identified ferroptosis as a central pathway mediating toxicity in both leachates. LAP exposure was associated with the upregulation of mt2 and fthl31 and the downregulation of slc40a1 suggesting disrupted iron metabolism and exacerbated oxidative damage. In contrast TWP exposure triggered adaptive responses including the upregulation of detoxification related genes such as cyp1a and gstt1b. These findings elucidate distinct toxicity mechanisms between TWP and LAP leachates and underscore the need for enhanced environmental monitoring and regulatory strategies to mitigate their ecological impacts.         CONTROL2   breed:AB|age:5 days|collection date:2024 05 26|geo loc name:Not collected|sex:Missing|tissue:Whole body|Replicate:Replicate = biological replicate 2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: zebrafish embryos CONTROL2 CONTROL2 mRNA seq of Danio rerio relication 2 of CONTROL     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP559953     CONTROL2.R1.raw.fastq.gz CONTROL2.R2.raw.fastq.gz fastq fastq 8261380328.0 27355564.0 CONTROL2.R1.raw.fastq.gz 0:151 1:151 A:2215199676;C:1884149053;G:1947224290;T:2214596047;N:211262 151 151     2215199676 1884149053 1947224290 2214596047 211262 SRX27476245 SRS23900294 SRA2060932 Qingdao University of Science and Technology|College of Marine Science and biological engineeri Qingdao University of Science and Technology                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-26 Larval Larval Trunk Surface Structure
34613 34613 SRR32129959 SRX27476244 SRS23900293 SRP559953 PRJNA1215813 Comparative Toxicological Effects of Tire Wear and Latex Particle Leachates in Zebrafish Embryos: Focus on Oxidative Stress and Ferroptosis PRJNA1215813 Other Microrubber a subset of microplastics has emerged as a significant environmental concern due to its persistence bioaccumulation and potential toxicity in aquatic ecosystems. This study investigates the toxicological effects of leachates derived from tire wear particles TWP and latex particles LAP on zebrafish embryos focusing on physiological oxidative stress and transcriptomic responses. LAP leachate exhibited significantly higher toxicity than TWP characterized by increased mortality delayed hatching reduced spontaneous movement suppressed heart rate and severe morphological malformations. Chemical analysis identified elevated levels of heavy metals and biologically active organic compounds with higher zinc concentrations and benzothiazole derivatives in LAP leachate contributing to its greater toxicity. Oxidative stress markers revealed elevated catalase CAT and malondialdehyde MDA levels in both groups but LAP exposure significantly reduced glutathione S transferase GST activity indicating compromised detoxification capacity. Transcriptomic analysis identified ferroptosis as a central pathway mediating toxicity in both leachates. LAP exposure was associated with the upregulation of mt2 and fthl31 and the downregulation of slc40a1 suggesting disrupted iron metabolism and exacerbated oxidative damage. In contrast TWP exposure triggered adaptive responses including the upregulation of detoxification related genes such as cyp1a and gstt1b. These findings elucidate distinct toxicity mechanisms between TWP and LAP leachates and underscore the need for enhanced environmental monitoring and regulatory strategies to mitigate their ecological impacts.         CONTROL1   breed:AB|age:5 days|collection date:2024 05 26|geo loc name:Not collected|sex:Missing|tissue:Whole body|Replicate:Replicate = biological replicate 1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: zebrafish embryos CONTROL1 CONTROL1 mRNA seq of Danio rerio relication 1 of CONTROL     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq X Plus   SRP559953     CONTROL1.R1.raw.fastq.gz CONTROL1.R2.raw.fastq.gz fastq fastq 7297086174.0 24162537.0 CONTROL1.R1.raw.fastq.gz 0:151 1:151 A:1869599378;C:1745386867;G:1807178668;T:1874732590;N:188671 151 151     1869599378 1745386867 1807178668 1874732590 188671 SRX27476244 SRS23900293 SRA2060932 Qingdao University of Science and Technology|College of Marine Science and biological engineeri Qingdao University of Science and Technology                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2025-01-26 Larval Larval Trunk Surface Structure
36223 36223 SRR33596639 SRX28826240 SRS25059183 SRP585802 PRJNA1263632 transcriptome analysis of cu693494.2 ORF3 mutant PRJNA1263632 Other The 3 dpf cu693494.2 ORF3 / and WT larvae were dark treated 1day and the zebrafish samples were collected at CT4/100 hpf each with duplicate samples.         cu ORF3 CT4 2   strain:AB|age:3 dpf|dev stage:100 hpf|collection date:2024 10 30|geo loc name:China:Suzhu|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: whole body treatment2 treatment2 RNA     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP585802     cu-orf3-ct4-2_L1_1.fq.gz cu-orf3-ct4-2_L1_2.fq.gz fastq fastq 6171131100.0 20570437.0 cu orf3 ct4 2 L1 1.fq.gz 0:150 1:150 A:1712348536;C:1373082573;G:1411350014;T:1674292589;N:57388 150 150     1712348536 1373082573 1411350014 1674292589 57388 SRX28826240 SRS25059183 SRA2130944 Soochow University|Center for Circadian Clocks Soochow University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Unknown 2025-05-16 Larval Larval Trunk Surface Structure
36224 36224 SRR33596640 SRX28826239 SRS25059182 SRP585802 PRJNA1263632 transcriptome analysis of cu693494.2 ORF3 mutant PRJNA1263632 Other The 3 dpf cu693494.2 ORF3 / and WT larvae were dark treated 1day and the zebrafish samples were collected at CT4/100 hpf each with duplicate samples.         cu ORF3 CT4 1   strain:AB|age:3 dpf|dev stage:100 hpf|collection date:2024 10 29|geo loc name:China:Suzhu|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: whole body treatment1 treatment1 RNA     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP585802     cu-orf3-ct4-1_L1_1.fq.gz cu-orf3-ct4-1_L1_2.fq.gz fastq fastq 5416142700.0 18053809.0 cu orf3 ct4 1 L1 1.fq.gz 0:150 1:150 A:1506288932;C:1201904939;G:1238064656;T:1469832889;N:51284 150 150     1506288932 1201904939 1238064656 1469832889 51284 SRX28826239 SRS25059182 SRA2130944 Soochow University|Center for Circadian Clocks Soochow University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Unknown 2025-05-16 Larval Larval Trunk Surface Structure
36225 36225 SRR33596641 SRX28826238 SRS25059181 SRP585802 PRJNA1263632 transcriptome analysis of cu693494.2 ORF3 mutant PRJNA1263632 Other The 3 dpf cu693494.2 ORF3 / and WT larvae were dark treated 1day and the zebrafish samples were collected at CT4/100 hpf each with duplicate samples.         WT CT4 2   strain:AB|age:3 dpf|dev stage:100 hpf|collection date:2024 10 28|geo loc name:China:Suzhu|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: whole body control2 control2 RNA     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP585802     wt-ct4-2_L1_1.fq.gz wt-ct4-2_L1_2.fq.gz fastq fastq 6965839200.0 23219464.0 wt ct4 2 L1 1.fq.gz 0:150 1:150 A:1904316669;C:1579337292;G:1621119016;T:1860980311;N:85912 150 150     1904316669 1579337292 1621119016 1860980311 85912 SRX28826238 SRS25059181 SRA2130944 Soochow University|Center for Circadian Clocks Soochow University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Unknown 2025-05-16 Larval Larval Trunk Surface Structure
36226 36226 SRR33596642 SRX28826237 SRS25059180 SRP585802 PRJNA1263632 transcriptome analysis of cu693494.2 ORF3 mutant PRJNA1263632 Other The 3 dpf cu693494.2 ORF3 / and WT larvae were dark treated 1day and the zebrafish samples were collected at CT4/100 hpf each with duplicate samples.         WT CT4 1   strain:AB|age:3 dpf|dev stage:100 hpf|collection date:2024 10 27|geo loc name:China:Suzhu|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: whole body control1 control1 RNA     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP585802     wt-ct4-1_L1_1.fq.gz wt-ct4-1_L1_2.fq.gz fastq fastq 5399973600.0 17999912.0 wt ct4 1 L1 1.fq.gz 0:150 1:150 A:1487700688;C:1212118655;G:1244330905;T:1455775411;N:47941 150 150     1487700688 1212118655 1244330905 1455775411 47941 SRX28826237 SRS25059180 SRA2130944 Soochow University|Center for Circadian Clocks Soochow University                       B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   Unknown 2025-05-16 Larval Larval Trunk Surface Structure
48054 48054 SRR7008006 SRX3940581 SRS3171382 SRP140462 PRJNA450341 Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling PRJNA450341 Other Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.     MO26h rep1 MO26h 1 Sample3   strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:fsd1morphants 1|BioSampleModel:Model organism or animal                 RNA seq of fsd1 morphants1 MO26h 1 MO26h 1 RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE BGISEQ BGISEQ-500   SRP140462     MO26h_1_1.fq.gz fastq 1193983450.0 23879669.0 MO26h 1 1.fq.gz 0:50 A:313344068;C:282899939;G:291404437;T:306051122;N:283884 50       313344068 282899939 291404437 306051122 283884 SRX3940581 SRS3171382 SRA690964 Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology Institute of Zoology, CHINESE ACADEMY OF SCIENCES 1 0.95658   0.07921   0.70307   0.47586   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2018-04-16 Pharyngula Embryo Trunk Surface Structure
48055 48055 SRR7008007 SRX3940580 SRS3171381 SRP140462 PRJNA450341 Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling PRJNA450341 Other Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.     MO26h rep2 MO26h 2 Sample4   strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:fsd1morphants 2|BioSampleModel:Model organism or animal                 RNA seq of fsd1 morphants2 MO26h 2 MO26h 2 RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE BGISEQ BGISEQ-500   SRP140462     MO26h_2_1.fq.gz fastq 1199524600.0 23990492.0 MO26h 2 1.fq.gz 0:50 A:318726410;C:282721669;G:287606979;T:310182197;N:287345 50       318726410 282721669 287606979 310182197 287345 SRX3940580 SRS3171381 SRA690964 Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology Institute of Zoology, CHINESE ACADEMY OF SCIENCES 1 0.9541   0.08695   0.70404   0.47195   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2018-04-16 Pharyngula Embryo Trunk Surface Structure
48056 48056 SRR7008008 SRX3940579 SRS3171379 SRP140462 PRJNA450341 Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling PRJNA450341 Other Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.     WT26h rep1 WT26h 1 Sample1   strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:normal embryos 1|BioSampleModel:Model organism or animal                 RNA seq of normal embryos1 WT26h 1 WT26h 1 RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE BGISEQ BGISEQ-500   SRP140462     WT26h_1_1.fq.gz fastq 1200268650.0 24005373.0 WT26h 1 1.fq.gz 0:50 A:315743815;C:284447849;G:295772915;T:303964473;N:339598 50       315743815 284447849 295772915 303964473 339598 SRX3940579 SRS3171379 SRA690964 Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology Institute of Zoology, CHINESE ACADEMY OF SCIENCES 1 0.95659   0.07726   0.70425   0.47269   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2018-04-16 Pharyngula Embryo Trunk Surface Structure
48057 48057 SRR7008009 SRX3940578 SRS3171380 SRP140462 PRJNA450341 Primary cilia regulate hematopoietic stem and progenitor cell specification through Notch signaling PRJNA450341 Other Hematopoietic stem and progenitor cells HSPCs are capable of producing all mature blood lineages as well as maintaining the self renewal ability throughout life. The hairy like organelle cilia are present in most types of vertebrate cells and play important roles in various biological processes. However it is unclear whether and how cilia regulate HSPC development in vertebrates. Here we show that cilia specific genes involved in primary cilia formation and signaling transduction are required for HSPC development especially at the hemogenic endothelium HE specification step in zebrafish embryos. Blocking primary cilia formation or function by genetic or chemical manipulations impaired HSPC development. Mechanistically we uncover that primary cilia on endothelial cells ECs transduce Notch signal to the earliest HE for proper HSPC specification during embryogenesis. Altogether our findings reveal a pivotal role of endothelial primary cilia in HSPC development and may shed lights into in vitro directed differentiation of HSPCs.     WT26h rep2 WT26h 2 Sample2   strain:zebrafish embryos|isolate:not applicable|dev stage:26 hpf|sex:not applicable|tissue:trunk region|collection date:2017 08 11|geo loc name:China: Beijing|isolation source:not applicable|sample type:normal embryos 2|BioSampleModel:Model organism or animal                 RNA seq of normal embryos2 WT26h 2 WT26h 2 RNA was isolated from trunk regions of control embryos and fsd1 morphants for cDNA library. The cDNA library for sequenced using BGISEQ 500 platform.     RNA-Seq TRANSCRIPTOMIC PCR SINGLE BGISEQ BGISEQ-500   SRP140462     WT26h_2_1.fq.gz fastq 1199179850.0 23983597.0 WT26h 2 1.fq.gz 0:50 A:316605984;C:281184572;G:292581373;T:308419476;N:388445 50       316605984 281184572 292581373 308419476 388445 SRX3940578 SRS3171380 SRA690964 Institute of Zoology, CHINESE ACADEMY OF SCIENCES|State Key Laboratory of Membrane Biology Institute of Zoology, CHINESE ACADEMY OF SCIENCES 1 0.95377   0.08617   0.70508   0.4775   50   B   usable mapping rate bgi bgi unknown random_priming unknown bulk unknown unknown   China 2018-04-16 Pharyngula Embryo Trunk Surface Structure
55219 55219 SRR10199007 SRX6919150 SRS5450113 SRP223586 PRJNA573544 Danio rerio strain:wild type AB Raw sequence reads PRJNA573544 Whole Genome Sequencing This study was designed to investigate the expression profiling when the target gene ZfXH was silenced. Two groups of zebrafishes ZfXH MO and Control MO were set. zebrafishes were injected with ZfXH MO and Control MO at one cell stage with 4ng MO respectively. Smaples were collected 3dpf and RNA was isolated. RNA was sequenced successfully.       Transcriptome isolated from Danio rerio ZfXH silenced Danio rerio   strain:wild type AB|age:3 dpf male and female|tissue:whole body of fish|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult tissue ZfXH MO ZfXH MO RNA seq     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP223586     ZfXH_MO_S21_L001_R1_001.fastq.gz ZfXH_MO_S21_L001_R2_001.fastq.gz fastq fastq 10018997678.0 33175489.0 ZfXH MO S21 L001 R1 001.fastq.gz 0:151 1:151 A:2631827404;C:2366264563;G:2402993536;T:2617896610;N:15565 151 151     2631827404 2366264563 2402993536 2617896610 15565 SRX6919150 SRS5450113 SRA969623 Institute of Fishery Sciences|Genetic Breeding and Healthy Aquaculture Institute of Fishery Sciences 2 0.95353 0.95357 0.09504 0.09477 0.67414 0.67452 0.4715 0.47446 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Unknown 2019-09-28 Larval Larval Trunk Surface Structure
55220 55220 SRR10199008 SRX6919149 SRS5450113 SRP223586 PRJNA573544 Danio rerio strain:wild type AB Raw sequence reads PRJNA573544 Whole Genome Sequencing This study was designed to investigate the expression profiling when the target gene ZfXH was silenced. Two groups of zebrafishes ZfXH MO and Control MO were set. zebrafishes were injected with ZfXH MO and Control MO at one cell stage with 4ng MO respectively. Smaples were collected 3dpf and RNA was isolated. RNA was sequenced successfully.       Transcriptome isolated from Danio rerio ZfXH silenced Danio rerio   strain:wild type AB|age:3 dpf male and female|tissue:whole body of fish|BioSampleModel:Model organism or animal                 RNA Seq of Danio rerio: adult tissue control MO control MO RNA seq     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA HiSeq X Ten   SRP223586     control_MO_S20_L001_R1_001.fastq.gz control_MO_S20_L001_R2_001.fastq.gz fastq fastq 8415899232.0 27867216.0 control MO S20 L001 R1 001.fastq.gz 0:151 1:151 A:2207602868;C:1993098209;G:2018109352;T:2197075569;N:13234 151 151     2207602868 1993098209 2018109352 2197075569 13234 SRX6919149 SRS5450113 SRA969623 Institute of Fishery Sciences|Genetic Breeding and Healthy Aquaculture Institute of Fishery Sciences 2 0.95324 0.953 0.0989 0.0986 0.66673 0.66683 0.47041 0.469 151 151 B B biological fallback assumption illumina hiseq_era unknown random_priming unknown bulk unknown unknown   Unknown 2019-09-28 Larval Larval Trunk Surface Structure
60116 60116 SRR13716596 SRX10105179 SRS8262182 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were exposed to 10oC for xxxh in the presence of 50 μM SB2035801 replicate #3 10C SB 3 10C SB 3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae exposed to 10oC in the presence of 50 μM SB203580|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 10C SB#3 10C SB#3 10C SB#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     10C-SB-3_L3_1.fq.gz 10C-SB-3_L3_2.fq.gz a10C-SB-3_L1_1.fq.gz a10C-SB-3_L1_2.fq.gz fastq fastq fastq fastq 6689447700.0 22298159.0 10C SB 3 L3 1.fq.gz 0:150 1:150 A:1755473088;C:1585054126;G:1622628538;T:1726253854;N:38094 150 150     1755473088 1585054126 1622628538 1726253854 38094 SRX10105179 SRS8262182 SRA1196485 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.92288 0.92244 0.08777 0.08783 0.67093 0.67067 0.47936 0.47997 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-16 Larval Larval Trunk Surface Structure
60117 60117 SRR13716597 SRX10105178 SRS8262180 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were exposed to 10oC for xxxh in the presence of 50 μM SB2035801 replicate #2 10C SB 2 10C SB 2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae exposed to 10oC in the presence of 50 μM SB203580|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 10C SB#2 10C SB#2 10C SB#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     10C-SB-2_L3_1.fq.gz 10C-SB-2_L3_2.fq.gz a10C-SB-2_L1_1.fq.gz a10C-SB-2_L1_2.fq.gz fastq fastq fastq fastq 6613801200.0 22046004.0 10C SB 2 L3 1.fq.gz 0:150 1:150 A:1718273446;C:1585274785;G:1621112738;T:1689101559;N:38672 150 150     1718273446 1585274785 1621112738 1689101559 38672 SRX10105178 SRS8262180 SRA1196485 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.92398 0.9243 0.08157 0.08161 0.67125 0.67006 0.48562 0.4718 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-16 Larval Larval Trunk Surface Structure
60118 60118 SRR13716598 SRX10105177 SRS8262181 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were exposed to 10oC for xxxh in the presence of 50 μM SB2035801 replicate #1 10C SB 1 10C SB 1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae exposed to 10oC in the presence of 50 μM SB203580|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 10C SB#1 10C SB#1 10C SB#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     10C-SB-1_L3_1.fq.gz 10C-SB-1_L3_2.fq.gz fastq fastq 5996072400.0 19986908.0 10C SB 1 L3 1.fq.gz 0:150 1:150 A:1548441285;C:1446480691;G:1472562271;T:1528551525;N:36628 150 150     1548441285 1446480691 1472562271 1528551525 36628 SRX10105177 SRS8262181 SRA1196485 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.92154 0.92139 0.07981 0.07967 0.66931 0.66776 0.48513 0.48473 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-16 Larval Larval Trunk Surface Structure
60119 60119 SRR13716310 SRX10104893 SRS8261917 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were exposed to 10oC for xxxh in the presence of 5 μM PD0325901 replicate #3 10C PD 3 10C PD 3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae exposed to 10oC in the presence of 5 μM PD0325901|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 10C PD#3 10C PD#3 10C PD#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     10C-PD-3_L3_1.fq.gz 10C-PD-3_L3_2.fq.gz a10C-PD-3_L1_1.fq.gz a10C-PD-3_L1_2.fq.gz fastq fastq fastq fastq 6553566900.0 21845223.0 10C PD 3 L3 1.fq.gz 0:150 1:150 A:1711712888;C:1560862189;G:1598014292;T:1682939768;N:37763 150 150     1711712888 1560862189 1598014292 1682939768 37763 SRX10104893 SRS8261917 SRA1196464 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.92319 0.92324 0.0836 0.08355 0.67306 0.67249 0.48209 0.47844 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-15 Larval Larval Trunk Surface Structure
60120 60120 SRR13716311 SRX10104892 SRS8261916 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were exposed to 10oC for xxxh in the presence of 5 μM PD0325901 replicate #2 10C PD 2 10C PD 2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae exposed to 10oC in the presence of 5 μM PD0325901|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 10C PD#2 10C PD#2 10C PD#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     10C-PD-2_L3_1.fq.gz 10C-PD-2_L3_2.fq.gz a10C-PD-2_L1_1.fq.gz a10C-PD-2_L1_2.fq.gz fastq fastq fastq fastq 6667400100.0 22224667.0 10C PD 2 L3 1.fq.gz 0:150 1:150 A:1751304072;C:1578216502;G:1613656813;T:1724183035;N:39678 150 150     1751304072 1578216502 1613656813 1724183035 39678 SRX10104892 SRS8261916 SRA1196464 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.92135 0.92072 0.08989 0.0899 0.66807 0.66722 0.48187 0.48732 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-15 Larval Larval Trunk Surface Structure
60121 60121 SRR13716312 SRX10104891 SRS8261915 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were exposed to 10oC for xxxh in the presence of 5 μM PD0325901 replicate #1 10C PD 1 10C PD 1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae exposed to 10oC in the presence of 5 μM PD0325901|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 10C PD#1 10C PD#1 10C PD#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     10C-PD-1_L3_1.fq.gz 10C-PD-1_L3_2.fq.gz fastq fastq 6443217000.0 21477390.0 10C PD 1 L3 1.fq.gz 0:150 1:150 A:1696055700;C:1522403644;G:1555774829;T:1668939971;N:42856 150 150     1696055700 1522403644 1555774829 1668939971 42856 SRX10104891 SRS8261915 SRA1196464 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.92085 0.92219 0.0928 0.09333 0.66405 0.66235 0.48345 0.48362 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-15 Larval Larval Trunk Surface Structure
60122 60122 SRR13708182 SRX10097122 SRS8254474 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were exposed to 10oC for xxxh in the presence of 0.5 μM AS1842856 replicate #3 10C AS 3 10C AS 3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae exposed to 10oC in the presence of 0.5 μM AS1842856|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 28C AS#3 10C AS#3 10C AS#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     10C-AS-3_L4_1.fq.gz 10C-AS-3_L4_2.fq.gz a10C-AS-3_L1_1.fq.gz a10C-AS-3_L1_2.fq.gz fastq fastq fastq fastq 6732036300.0 22440121.0 10C AS 3 L4 1.fq.gz 0:150 1:150 A:1784280791;C:1573905995;G:1615796221;T:1758043122;N:10171 150 150     1784280791 1573905995 1615796221 1758043122 10171 SRX10097122 SRS8254474 SRA1196187 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.92104 0.92236 0.0898 0.0901 0.66979 0.66961 0.48787 0.48861 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-14 Larval Larval Trunk Surface Structure
60123 60123 SRR13708183 SRX10097121 SRS8254473 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were exposed to 10oC for xxxh in the presence of 0.5 μM AS1842856 replicate #2 10C AS 2 10C AS 2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae exposed to 10oC in the presence of 0.5 μM AS1842856|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 28C AS#2 10C AS#2 10C AS#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     10C-AS-2_L3_1.fq.gz 10C-AS-2_L3_2.fq.gz fastq fastq 5996978400.0 19989928.0 10C AS 2 L3 1.fq.gz 0:150 1:150 A:1586465143;C:1405066884;G:1448159164;T:1557252287;N:34922 150 150     1586465143 1405066884 1448159164 1557252287 34922 SRX10097121 SRS8254473 SRA1196187 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.91787 0.91834 0.08889 0.08892 0.6692 0.66898 0.48573 0.48749 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-14 Larval Larval Trunk Surface Structure
60124 60124 SRR13708184 SRX10097120 SRS8254472 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were exposed to 10oC for xxxh in the presence of 0.5 μM AS1842856 replicate #1 10C AS 1 10C AS 1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae exposed to 10oC in the presence of 0.5 μM AS1842856|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 28C AS#1 10C AS#1 10C AS#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     10C-AS-1_L3_1.fq.gz 10C-AS-1_L3_2.fq.gz a10C-AS-1_L1_1.fq.gz a10C-AS-1_L1_2.fq.gz fastq fastq fastq fastq 6569816400.0 21899388.0 10C AS 1 L3 1.fq.gz 0:150 1:150 A:1737515846;C:1540816249;G:1582569507;T:1708881397;N:33401 150 150     1737515846 1540816249 1582569507 1708881397 33401 SRX10097120 SRS8254472 SRA1196187 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.91936 0.92032 0.08712 0.08707 0.66849 0.66697 0.49092 0.49151 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-14 Larval Larval Trunk Surface Structure
60125 60125 SRR13707161 SRX10096101 SRS8253483 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were exposed to 10oC for xxxh in the presence of 1/1000 DMSO replicate #3 10C DMSO 3 10C DMSO 3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae exposed to 10oC in the presence of 1/1000 DMSO|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 28C AS#3 10C DMSO#3 10C DMSO#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     10C-DMSO-3_L3_1.fq.gz 10C-DMSO-3_L3_2.fq.gz fastq fastq 5904314400.0 19681048.0 10C DMSO 3 L3 1.fq.gz 0:150 1:150 A:1539151362;C:1409713024;G:1445164550;T:1510248421;N:37043 150 150     1539151362 1409713024 1445164550 1510248421 37043 SRX10096101 SRS8253483 SRA1196168 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93032 0.93038 0.08225 0.08242 0.67282 0.67168 0.47769 0.48048 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-14 Larval Larval Trunk Surface Structure
60126 60126 SRR13707162 SRX10096100 SRS8253482 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were exposed to 10oC for xxxh in the presence of 1/1000 DMSO replicate #2 10C DMSO 2 10C DMSO 2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae exposed to 10oC in the presence of 1/1000 DMSO|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 28C AS#2 10C DMSO#2 10C DMSO#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     10C-DMSO-2_L3_1.fq.gz 10C-DMSO-2_L3_2.fq.gz fastq fastq 6006327900.0 20021093.0 10C DMSO 2 L3 1.fq.gz 0:150 1:150 A:1569204011;C:1431943938;G:1467115626;T:1538025449;N:38876 150 150     1569204011 1431943938 1467115626 1538025449 38876 SRX10096100 SRS8253482 SRA1196168 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.92966 0.93003 0.08607 0.08623 0.66947 0.66935 0.47981 0.47923 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-14 Larval Larval Trunk Surface Structure
60127 60127 SRR13707163 SRX10096099 SRS8253481 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were exposed to 10oC for xxxh in the presence of 1/1000 DMSO replicate #1 10C DMSO 1 10C DMSO 1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae exposed to 10oC in the presence of 1/1000 DMSO|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 28C AS#1 10C DMSO#1 10C DMSO#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     10C-DMSO-1_L3_1.fq.gz 10C-DMSO-1_L3_2.fq.gz fastq fastq 6056499000.0 20188330.0 10C DMSO 1 L3 1.fq.gz 0:150 1:150 A:1537475715;C:1487268906;G:1523545020;T:1508171266;N:38093 150 150     1537475715 1487268906 1523545020 1508171266 38093 SRX10096099 SRS8253481 SRA1196168 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93554 0.93577 0.06971 0.06986 0.67308 0.67129 0.48422 0.47976 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-14 Larval Larval Trunk Surface Structure
60128 60128 SRR13706208 SRX10095148 SRS8252537 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were treated with 50 μM SB203580 for 12h at normal temperature replicate #3 28C SB 3 28C SB 3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae treated with 50 μM SB203580 at normal temperature|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 28C AS#3 28C SB#3 28C SB#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     28C-SB-3_L3_1.fq.gz 28C-SB-3_L3_2.fq.gz a28C-SB-3_L1_1.fq.gz a28C-SB-3_L1_2.fq.gz fastq fastq fastq fastq 6594180900.0 21980603.0 28C SB 3 L3 1.fq.gz 0:150 1:150 A:1689900125;C:1600654190;G:1651026430;T:1652552026;N:48129 150 150     1689900125 1600654190 1651026430 1652552026 48129 SRX10095148 SRS8252537 SRA1196134 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93294 0.93276 0.05921 0.05915 0.66543 0.66492 0.47486 0.47492 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-13 Larval Larval Trunk Surface Structure
60129 60129 SRR13706209 SRX10095147 SRS8252536 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were treated with 50 μM SB203580 for 12h at normal temperature replicate #2 28C SB 2 28C SB 2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae treated with 50 μM SB203580 at normal temperature|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 28C AS#2 28C SB#2 28C SB#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     28C-SB-2_L3_1.fq.gz 28C-SB-2_L3_2.fq.gz a28C-SB-2_L1_1.fq.gz a28C-SB-2_L1_2.fq.gz fastq fastq fastq fastq 6503823300.0 21679411.0 28C SB 2 L3 1.fq.gz 0:150 1:150 A:1671366325;C:1574642308;G:1618319340;T:1639451188;N:44139 150 150     1671366325 1574642308 1618319340 1639451188 44139 SRX10095147 SRS8252536 SRA1196134 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.9316 0.93174 0.06054 0.06095 0.66192 0.66253 0.48331 0.48394 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-13 Larval Larval Trunk Surface Structure
60130 60130 SRR13706210 SRX10095146 SRS8252535 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were treated with 50 μM SB203580 for 12h at normal temperature replicate #1 28C SB 1 28C SB 1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae treated with 50 μM SB203580 at normal temperature|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 28C AS#1 28C SB#1 28C SB#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     28C-SB-1_L3_1.fq.gz 28C-SB-1_L3_2.fq.gz a28C-SB-1_L1_1.fq.gz a28C-SB-1_L1_2.fq.gz fastq fastq fastq fastq 6433728600.0 21445762.0 28C SB 1 L3 1.fq.gz 0:150 1:150 A:1644012802;C:1567311809;G:1617097059;T:1605256226;N:50704 150 150     1644012802 1567311809 1617097059 1605256226 50704 SRX10095146 SRS8252535 SRA1196134 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93588 0.93579 0.05578 0.05595 0.66738 0.66691 0.4704 0.47338 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-13 Larval Larval Trunk Surface Structure
60131 60131 SRR13705396 SRX10094348 SRS8251794 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were treated with 5 μM PD0325901 for 12h at normal temperature replicate #3 28C PD 3 28C PD 3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae treated with 5 μM PD0325901 at normal temperature|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 28C AS#3 28C PD#3 28C PD#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     28C-PD-3_L3_1.fq.gz 28C-PD-3_L3_2.fq.gz a28C-PD-3_L1_1.fq.gz a28C-PD-3_L1_2.fq.gz fastq fastq fastq fastq 6316603200.0 21055344.0 28C PD 3 L3 1.fq.gz 0:150 1:150 A:1623963129;C:1530460527;G:1575145519;T:1586988238;N:45787 150 150     1623963129 1530460527 1575145519 1586988238 45787 SRX10094348 SRS8251794 SRA1195973 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93748 0.93754 0.06126 0.06113 0.66255 0.6621 0.46522 0.46708 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-13 Larval Larval Trunk Surface Structure
60132 60132 SRR13705397 SRX10094347 SRS8251793 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were treated with 5 μM PD0325901 for 12h at normal temperature replicate #2 28C PD 2 28C PD 2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae treated with 5 μM PD0325901 at normal temperature|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 28C AS#2 28C PD#2 28C PD#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     28C-PD-2_L3_1.fq.gz 28C-PD-2_L3_2.fq.gz a28C-PD-2_L1_1.fq.gz a28C-PD-2_L1_2.fq.gz fastq fastq fastq fastq 6415971300.0 21386571.0 28C PD 2 L3 1.fq.gz 0:150 1:150 A:1653125594;C:1551175406;G:1593234041;T:1618387048;N:49211 150 150     1653125594 1551175406 1593234041 1618387048 49211 SRX10094347 SRS8251793 SRA1195973 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93614 0.93566 0.06336 0.06349 0.65896 0.65847 0.47393 0.47942 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-13 Larval Larval Trunk Surface Structure
60133 60133 SRR13705398 SRX10094346 SRS8251792 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were treated with 5 μM PD0325901 for 12h at normal temperature replicate #1 28C PD 1 28C PD 1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae treated with 5 μM PD0325901 at normal temperature|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 28C AS#1 28C PD#1 28C PD#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     28C-PD-1_L3_1.fq.gz 28C-PD-1_L3_2.fq.gz a28C-PD-1_L1_1.fq.gz a28C-PD-1_L1_2.fq.gz fastq fastq fastq fastq 6316612500.0 21055375.0 28C PD 1 L3 1.fq.gz 0:150 1:150 A:1625594742;C:1529992924;G:1568064215;T:1592911190;N:49429 150 150     1625594742 1529992924 1568064215 1592911190 49429 SRX10094346 SRS8251792 SRA1195973 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93445 0.93499 0.06232 0.06241 0.65926 0.6594 0.47641 0.47414 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-13 Larval Larval Trunk Surface Structure
60134 60134 SRR13674719 SRX10064162 SRS8226292 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were treated with 0.5 μM AS1842856 for 12h at normal temperature replicate #3 28C AS 3 28C AS 3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae treated with 0.5 μM AS1842856 at normal temperature|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 28C AS#3 28C AS#3 28C AS#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     a28C-AS-3_L1_2.fq.gz a28C-AS-3_L1_1.fq.gz 28C-AS-3_L3_2.fq.gz 28C-AS-3_L3_1.fq.gz fastq fastq fastq fastq 6808865100.0 22696217.0 28C AS 3 L3 1.fq.gz 0:150 1:150 A:1771098634;C:1630525561;G:1661862192;T:1745324102;N:54611 150 150     1771098634 1630525561 1661862192 1745324102 54611 SRX10064162 SRS8226292 SRA1194325 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93377 0.934 0.06494 0.06526 0.66705 0.6664 0.48432 0.48396 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-10 Larval Larval Trunk Surface Structure
60135 60135 SRR13674720 SRX10064161 SRS8226291 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were treated with 0.5 μM AS1842856 for 12h at normal temperature replicate #2 28C AS 2 28C AS 2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae treated with 0.5 μM AS1842856 at normal temperature|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 28C AS#2 28C AS#2 28C AS#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     a28C-AS-2_L1_2.fq.gz a28C-AS-2_L1_1.fq.gz 28C-AS-2_L3_2.fq.gz 28C-AS-2_L3_1.fq.gz fastq fastq fastq fastq 6814335000.0 22714450.0 28C AS 2 L3 1.fq.gz 0:150 1:150 A:1761654071;C:1642988616;G:1682689927;T:1726945565;N:56821 150 150     1761654071 1642988616 1682689927 1726945565 56821 SRX10064161 SRS8226291 SRA1194325 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93541 0.93539 0.06484 0.06484 0.66661 0.66624 0.48349 0.48748 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-10 Larval Larval Trunk Surface Structure
60136 60136 SRR13674721 SRX10064160 SRS8226290 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were treated with 0.5 μM AS1842856 for 12h at normal temperature replicate #1 28C AS 1 28C AS 1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Zebrafish larvae treated with 0.5 μM AS1842856 at normal temperature|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 28C AS#1 28C AS#1 28C AS#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     28C-AS-1_L3_1.fq.gz 28C-AS-1_L3_2.fq.gz a28C-AS-1_L1_1.fq.gz a28C-AS-1_L1_2.fq.gz fastq fastq fastq fastq 6824750400.0 22749168.0 28C AS 1 L3 1.fq.gz 0:150 1:150 A:1770677413;C:1638137834;G:1678636890;T:1737243815;N:54448 150 150     1770677413 1638137834 1678636890 1737243815 54448 SRX10064160 SRS8226290 SRA1194325 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93454 0.93398 0.06331 0.06325 0.66578 0.66523 0.49519 0.4905 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-10 Larval Larval Trunk Surface Structure
60137 60137 SRR13674523 SRX10063966 SRS8226108 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were maintained at 28oC for 12h in the presence of 1/1000 DMSO replicate #3 28C DMSO 3 28C DMSO 3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Vehicle control maintained at normal temperature|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 28C DMSO#3 28C DMSO#3 28C DMSO#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     28C-DMSO-3_L3_1.fq.gz 28C-DMSO-3_L3_2.fq.gz a28C-DMSO-3_L1_1.fq.gz a28C-DMSO-3_L1_2.fq.gz fastq fastq fastq fastq 6271525200.0 20905084.0 28C DMSO 3 L3 1.fq.gz 0:150 1:150 A:1611660004;C:1518014092;G:1561398402;T:1580403620;N:49082 150 150     1611660004 1518014092 1561398402 1580403620 49082 SRX10063966 SRS8226108 SRA1194314 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93493 0.9345 0.05642 0.05649 0.66184 0.66113 0.48122 0.48274 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-10 Larval Larval Trunk Surface Structure
60138 60138 SRR13674524 SRX10063965 SRS8226107 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were maintained at 28oC for 12h in the presence of 1/1000 DMSO replicate #2 28C DMSO 2 28C DMSO 2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Vehicle control maintained at normal temperature|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 28C DMSO#2 28C DMSO#2 28C DMSO#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     28C-DMSO-2_L3_1.fq.gz 28C-DMSO-2_L3_2.fq.gz a28C-DMSO-2_L1_1.fq.gz a28C-DMSO-2_L1_2.fq.gz fastq fastq fastq fastq 6586296900.0 21954323.0 28C DMSO 2 L3 1.fq.gz 0:150 1:150 A:1694478032;C:1592807476;G:1640193640;T:1658780401;N:37351 150 150     1694478032 1592807476 1640193640 1658780401 37351 SRX10063965 SRS8226107 SRA1194314 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93432 0.9342 0.05657 0.05627 0.66194 0.66093 0.48074 0.47814 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-10 Larval Larval Trunk Surface Structure
60139 60139 SRR13674525 SRX10063964 SRS8226106 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     The larvae at 96hpf were maintained at 28oC for 12h in the presence of 1/1000 DMSO replicate #1 28C DMSO 1 28C DMSO 1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Vehicle control maintained at normal temperature|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 28C DMSO#1 28C DMSO#1 28C DMSO#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     28C-DMSO-1_L3_1.fq.gz 28C-DMSO-1_L3_2.fq.gz fastq fastq 5969692800.0 19898976.0 28C DMSO 1 L3 1.fq.gz 0:150 1:150 A:1502645256;C:1475802063;G:1526815454;T:1464391541;N:38486 150 150     1502645256 1475802063 1526815454 1464391541 38486 SRX10063964 SRS8226106 SRA1194314 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93979 0.94082 0.0485 0.04881 0.66854 0.66695 0.47722 0.47801 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-10 Larval Larval Trunk Surface Structure
60140 60140 SRR13673980 SRX10063423 SRS8225646 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Wild type larvae at 97 hpf replicate #3 96hpf 3 96hpf 3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Wild type zebrafish larvae at 98hpf|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 96hpf#3 96hpf#3 96hpf#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     96hpf-3_L1_1.fq.gz 96hpf-3_L1_2.fq.gz a96hpf-3_L1_1.fq.gz a96hpf-3_L1_2.fq.gz fastq fastq fastq fastq 6812021700.0 22706739.0 96hpf 3 L1 1.fq.gz 0:150 1:150 A:1769209232;C:1632156904;G:1670117160;T:1740527062;N:11342 150 150     1769209232 1632156904 1670117160 1740527062 11342 SRX10063423 SRS8225646 SRA1194287 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93082 0.93281 0.06403 0.06382 0.65983 0.65977 0.4805 0.48038 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-09 Larval Larval Trunk Surface Structure
60141 60141 SRR13673981 SRX10063422 SRS8225645 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Wild type larvae at 97 hpf replicate #2 96hpf 2 96hpf 2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Wild type zebrafish larvae at 97hpf|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 96hpf#2 96hpf#2 96hpf#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     96hpf-2_L3_1.fq.gz 96hpf-2_L3_2.fq.gz a96hpf-2_L1_1.fq.gz a96hpf-2_L1_2.fq.gz fastq fastq fastq fastq 6754691700.0 22515639.0 96hpf 2 L3 1.fq.gz 0:150 1:150 A:1745293298;C:1627457133;G:1675487910;T:1706401036;N:52323 150 150     1745293298 1627457133 1675487910 1706401036 52323 SRX10063422 SRS8225645 SRA1194287 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93414 0.93476 0.05871 0.05862 0.66068 0.65983 0.48441 0.47805 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-09 Larval Larval Trunk Surface Structure
60142 60142 SRR13673982 SRX10063421 SRS8225644 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Wild type larvae at 97 hpf replicate #1 96hpf 1 96hpf 1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:Wild type zebrafish larvae at 96hpf|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 96hpf#1 96hpf#1 96hpf#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     96hpf-1_L3_1.fq.gz 96hpf-1_L3_2.fq.gz a96hpf-1_L1_1.fq.gz a96hpf-1_L1_2.fq.gz fastq fastq fastq fastq 6277755900.0 20925853.0 96hpf 1 L3 1.fq.gz 0:150 1:150 A:1629739306;C:1504852773;G:1548656411;T:1594457255;N:50155 150 150     1629739306 1504852773 1548656411 1594457255 50155 SRX10063421 SRS8225644 SRA1194287 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.93537 0.93562 0.06431 0.06474 0.65553 0.65547 0.47983 0.46402 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2021-02-09 Larval Larval Trunk Surface Structure
60143 60143 SRR12201939 SRX8712806 SRS6988633 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 24h recovery at normal temperature replicate #2 re 24h#2 re 24h#2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 24h|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 re 24h#2 re 24h#2 re 24h#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T114_good_1.fq.gz Zebrafish_N082-01-T114_good_2.fq.gz fastq fastq 8951725974.0 30043805.0 Zebrafish N082 01 T114 good 1.fq.gz 0:148.98 1:148.98 A:2286271179;C:2194588496;G:2204671632;T:2266185827;N:8840 148 148     2286271179 2194588496 2204671632 2266185827 8840 SRX8712806 SRS6988633 SRA1097872 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94891 0.95075 0.0598 0.06016 0.65752 0.65794 0.46576 0.46511 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-12 Larval Larval Trunk Surface Structure
60144 60144 SRR12201940 SRX8712805 SRS6988632 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 24h recovery at normal temperature replicate #1 re 24h#1 re 24h#1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 24h|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 re 24h#1 re 24h#1 re 24h#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T113_good_1.fq.gz Zebrafish_N082-01-T113_good_2.fq.gz fastq fastq 7958555272.0 26704073.0 Zebrafish N082 01 T113 good 1.fq.gz 0:149.01 1:149.01 A:2023637490;C:1960455575;G:1968384676;T:2006069808;N:7723 149 149     2023637490 1960455575 1968384676 2006069808 7723 SRX8712805 SRS6988632 SRA1097872 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94834 0.95018 0.05788 0.05807 0.66151 0.66103 0.46366 0.46419 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-12 Larval Larval Trunk Surface Structure
60145 60145 SRR12201941 SRX8712804 SRS6988631 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 24h recovery at normal temperature replicate #3 re 24h#3 re 24h#3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 24h|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 re 24h#3 re 24h#3 re 24h#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T115_good_1.fq.gz Zebrafish_N082-01-T115_good_2.fq.gz fastq fastq 8670551476.0 29052478.0 Zebrafish N082 01 T115 good 1.fq.gz 0:149.22 1:149.22 A:2212292115;C:2127883525;G:2138942171;T:2191425359;N:8306 149 149     2212292115 2127883525 2138942171 2191425359 8306 SRX8712804 SRS6988631 SRA1097872 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94881 0.95013 0.06047 0.06052 0.65916 0.65865 0.46098 0.46284 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-12 Larval Larval Trunk Surface Structure
60146 60146 SRR12201912 SRX8712779 SRS6988606 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 12h recovery at normal temperature replicate #2 re 12h#2 re 12h#2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 12h|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 re 12h#2 re 12h#2 re 12h#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T111_good_1.fq.gz Zebrafish_N082-01-T111_good_2.fq.gz fastq fastq 8699622392.0 29153677.0 Zebrafish N082 01 T111 good 1.fq.gz 0:149.20 1:149.20 A:2219401729;C:2136842246;G:2144939919;T:2198430097;N:8401 149 149     2219401729 2136842246 2144939919 2198430097 8401 SRX8712779 SRS6988606 SRA1097867 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94835 0.95109 0.05974 0.0604 0.6546 0.65421 0.46714 0.46221 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-12 Larval Larval Trunk Surface Structure
60147 60147 SRR12201913 SRX8712778 SRS6988605 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 12h recovery at normal temperature replicate #1 re 12h#1 re 12h#1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 12h|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 re 12h#1 re 12h#1 re 12h#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T110_good_1.fq.gz Zebrafish_N082-01-T110_good_2.fq.gz fastq fastq 9659696198.0 32399989.0 Zebrafish N082 01 T110 good 1.fq.gz 0:149.07 1:149.07 A:2484585860;C:2352819432;G:2361786076;T:2460495280;N:9550 149 149     2484585860 2352819432 2361786076 2460495280 9550 SRX8712778 SRS6988605 SRA1097867 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94796 0.94987 0.06359 0.06391 0.65453 0.65484 0.46234 0.46449 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-12 Larval Larval Trunk Surface Structure
60148 60148 SRR12201914 SRX8712777 SRS6988604 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 12h recovery at normal temperature replicate #3 re 12h#3 re 12h#3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 12h|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 re 12h#3 re 12h#3 re 12h#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T112_good_1.fq.gz Zebrafish_N082-01-T112_good_2.fq.gz fastq fastq 9530465006.0 31967666.0 Zebrafish N082 01 T112 good 1.fq.gz 0:149.06 1:149.06 A:2430778988;C:2340273985;G:2350943720;T:2408458634;N:9679 149 149     2430778988 2340273985 2350943720 2408458634 9679 SRX8712777 SRS6988604 SRA1097867 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94825 0.94934 0.0598 0.05972 0.65758 0.65703 0.45921 0.46577 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-12 Larval Larval Trunk Surface Structure
60149 60149 SRR12201311 SRX8712178 SRS6988102 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 6h recovery at normal temperature replicate #3 re 6h#3 re 6h#3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 6h|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 re 6h#3 re 6h#3 re 6h#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T109_good_1.fq.gz Zebrafish_N082-01-T109_good_2.fq.gz fastq fastq 8656222216.0 29119374.0 Zebrafish N082 01 T109 good 1.fq.gz 0:148.63 1:148.63 A:2224288504;C:2107136529;G:2119597196;T:2205191367;N:8620 148 148     2224288504 2107136529 2119597196 2205191367 8620 SRX8712178 SRS6988102 SRA1097851 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94918 0.9507 0.06678 0.06714 0.65105 0.65109 0.46125 0.46263 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-11 Larval Larval Trunk Surface Structure
60150 60150 SRR12201312 SRX8712177 SRS6988101 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 6h recovery at normal temperature replicate #2 re 6h#2 re 6h#2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 6h|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 re 6h#2 re 6h#2 re 6h#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T108_good_1.fq.gz Zebrafish_N082-01-T108_good_2.fq.gz fastq fastq 9145523612.0 30667280.0 Zebrafish N082 01 T108 good 1.fq.gz 0:149.11 1:149.11 A:2318208147;C:2256664707;G:2271799033;T:2298842568;N:9157 149 149     2318208147 2256664707 2271799033 2298842568 9157 SRX8712177 SRS6988101 SRA1097851 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94948 0.95136 0.05787 0.05778 0.65529 0.65486 0.46308 0.46219 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-11 Larval Larval Trunk Surface Structure
60151 60151 SRR12201313 SRX8712176 SRS6988100 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 6h recovery at normal temperature replicate #1 re 6h#1 re 6h#1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 6h|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 re 6h#1 re 6h#1 re 6h#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T107_good_1.fq.gz Zebrafish_N082-01-T107_good_2.fq.gz fastq fastq 9926776130.0 33299889.0 Zebrafish N082 01 T107 good 1.fq.gz 0:149.05 1:149.05 A:2517844728;C:2449564536;G:2462487965;T:2496869115;N:9786 149 149     2517844728 2449564536 2462487965 2496869115 9786 SRX8712176 SRS6988100 SRA1097851 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.9487 0.95018 0.05888 0.05881 0.65646 0.65593 0.46185 0.46088 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-11 Larval Larval Trunk Surface Structure
60152 60152 SRR12199231 SRX8710112 SRS6986609 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 2h recovery at normal temperature replicate #3 re 2h#3 re 2h#3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 2h|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 re 2h#3 re 2h#3 re 2h#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T106_good_1.fq.gz Zebrafish_N082-01-T106_good_2.fq.gz fastq fastq 9253109430.0 31027133.0 Zebrafish N082 01 T106 good 1.fq.gz 0:149.11 1:149.11 A:2356214864;C:2275049635;G:2285941834;T:2335893825;N:9272 149 149     2356214864 2275049635 2285941834 2335893825 9272 SRX8710112 SRS6986609 SRA1097576 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.95103 0.95264 0.06133 0.06212 0.66413 0.66448 0.45692 0.45955 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-11 Larval Larval Trunk Surface Structure
60153 60153 SRR12199232 SRX8710111 SRS6986608 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 2h recovery at normal temperature replicate #2 re 2h#2 re 2h#2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 2h|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 re 2h#2 re 2h#2 re 2h#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T105_good_1.fq.gz Zebrafish_N082-01-T105_good_2.fq.gz fastq fastq 7648566586.0 25649463.0 Zebrafish N082 01 T105 good 1.fq.gz 0:149.10 1:149.10 A:1948929425;C:1879144940;G:1888918416;T:1931566315;N:7490 149 149     1948929425 1879144940 1888918416 1931566315 7490 SRX8710111 SRS6986608 SRA1097576 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.95035 0.95278 0.05867 0.05916 0.66555 0.6644 0.47121 0.47186 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-11 Larval Larval Trunk Surface Structure
60154 60154 SRR12199233 SRX8710110 SRS6986607 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 2h recovery at normal temperature replicate #1 re 2h#1 re 2h#1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 2h|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 re 2h#1 re 2h#1 re 2h#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T104_good_1.fq.gz Zebrafish_N082-01-T104_good_2.fq.gz fastq fastq 10224077862.0 34273410.0 Zebrafish N082 01 T104 good 1.fq.gz 0:149.15 1:149.15 A:2604294955;C:2511336108;G:2527667881;T:2580768866;N:10052 149 149     2604294955 2511336108 2527667881 2580768866 10052 SRX8710110 SRS6986607 SRA1097576 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94893 0.94947 0.06454 0.06467 0.66326 0.66172 0.45924 0.46082 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-11 Larval Larval Trunk Surface Structure
60155 60155 SRR12197603 SRX8709604 SRS6986185 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Normal fish post exposed to lethal cold stress for 24h and recoverd at normal temperature for xxxh replicate #4 er nor#3 er nor#3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:normal|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 ctrl 97hpf#3 er nor#3 er nor#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T172_good_1.fq.gz Zebrafish_N082-01-T172_good_2.fq.gz fastq fastq 8506554192.0 28533509.0 Zebrafish N082 01 T172 good 1.fq.gz 0:149.06 1:149.06 A:2176028633;C:2082458309;G:2097709085;T:2150238585;N:119580 149 149     2176028633 2082458309 2097709085 2150238585 119580 SRX8709604 SRS6986185 SRA1097465 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94761 0.94975 0.06067 0.06061 0.65419 0.65443 0.46579 0.47525 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-10 Larval Larval Trunk Surface Structure
60156 60156 SRR12197604 SRX8709603 SRS6986184 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Normal fish post exposed to lethal cold stress for 24h and recoverd at normal temperature for xxxh replicate #2 er nor#2 er nor#2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:normal|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 ctrl 97hpf#2 er nor#2 er nor#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T171_good_1.fq.gz Zebrafish_N082-01-T171_good_2.fq.gz fastq fastq 8995710992.0 30173073.0 Zebrafish N082 01 T171 good 1.fq.gz 0:149.07 1:149.07 A:2298230118;C:2204887359;G:2220602724;T:2271866881;N:123910 149 149     2298230118 2204887359 2220602724 2271866881 123910 SRX8709603 SRS6986184 SRA1097465 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94658 0.94876 0.06217 0.06237 0.65502 0.65451 0.46687 0.46747 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-10 Larval Larval Trunk Surface Structure
60157 60157 SRR12197605 SRX8709602 SRS6986183 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Normal fish post exposed to lethal cold stress for 24h and recoverd at normal temperature for xxxh replicate #1 er nor#1 er nor#1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:normal|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 ctrl 97hpf#1 er nor#1 er nor#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T170_good_2.fq.gz Zebrafish_N082-01-T170_good_1.fq.gz fastq fastq 7506044838.0 25191768.0 Zebrafish N082 01 T170 good 1.fq.gz 0:148.98 1:148.98 A:1914522378;C:1840442485;G:1855580567;T:1895395505;N:103903 148 148     1914522378 1840442485 1855580567 1895395505 103903 SRX8709602 SRS6986183 SRA1097465 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94858 0.95019 0.05917 0.05953 0.65837 0.65685 0.4702 0.46832 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-10 Larval Larval Trunk Surface Structure
60158 60158 SRR12191835 SRX8705682 SRS6982492 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Abnormal fish post exposed to lethal cold stress for 24h and recoverd at normal temperature for xxxh replicate #4 er ab#3 er ab#3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:abnormal|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 er ab#3 er ab#3 er ab#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T169_good_2.fq.gz Zebrafish_N082-01-T169_good_1.fq.gz fastq fastq 7400288962.0 24803845.0 Zebrafish N082 01 T169 good 1.fq.gz 0:149.18 1:149.18 A:1888611369;C:1816077248;G:1829706730;T:1865791682;N:101933 149 149     1888611369 1816077248 1829706730 1865791682 101933 SRX8705682 SRS6982492 SRA1097128 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94615 0.94906 0.05988 0.06026 0.662 0.66109 0.4534 0.47434 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-10 Larval Larval Trunk Surface Structure
60159 60159 SRR12191836 SRX8705681 SRS6982491 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Abnormal fish post exposed to lethal cold stress for 24h and recoverd at normal temperature for xxxh replicate #2 er ab#2 er ab#2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:abnormal|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 er ab#2 er ab#2 er ab#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T168_good_1.fq.gz Zebrafish_N082-01-T168_good_2.fq.gz fastq fastq 10546122692.0 35346908.0 Zebrafish N082 01 T168 good 1.fq.gz 0:149.18 1:149.18 A:2699665940;C:2580731900;G:2597823661;T:2667754621;N:146570 149 149     2699665940 2580731900 2597823661 2667754621 146570 SRX8705681 SRS6982491 SRA1097128 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.9485 0.95097 0.05885 0.05928 0.65585 0.65587 0.46413 0.46489 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-10 Larval Larval Trunk Surface Structure
60160 60160 SRR12191837 SRX8705680 SRS6982490 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Abnormal fish post exposed to lethal cold stress for 24h and recoverd at normal temperature for xxxh replicate #1 er ab#1 er ab#1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:abnormal|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 er ab#1 er ab#1 er ab#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T167_good_2.fq.gz Zebrafish_N082-01-T167_good_1.fq.gz fastq fastq 8434638850.0 28264052.0 Zebrafish N082 01 T167 good 1.fq.gz 0:149.21 1:149.21 A:2154726978;C:2069246532;G:2081632624;T:2128914722;N:117994 149 149     2154726978 2069246532 2081632624 2128914722 117994 SRX8705680 SRS6982490 SRA1097128 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94793 0.95053 0.06213 0.06244 0.65764 0.65815 0.45875 0.46018 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-10 Larval Larval Trunk Surface Structure
60161 60161 SRR12191838 SRX8705679 SRS6982489 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh replicate #3 lc 24h#3 lc 24h#3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:lethal cold stress 24h|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 ctrl 97hpf#3 lc 24h#3 lc 24h#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T175_good_2.fq.gz Zebrafish_N082-01-T175_good_1.fq.gz fastq fastq 9280492948.0 31195529.0 Zebrafish N082 01 T175 good 1.fq.gz 0:148.75 1:148.75 A:2375701991;C:2270956127;G:2279790199;T:2353943787;N:100844 148 148     2375701991 2270956127 2279790199 2353943787 100844 SRX8705679 SRS6982489 SRA1097128 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94745 0.9494 0.07774 0.07799 0.68448 0.68304 0.46847 0.46697 140 140 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-10 Larval Larval Trunk Surface Structure
60162 60162 SRR12191839 SRX8705678 SRS6982488 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh replicate #2 lc 24h#2 lc 24h#2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:lethal cold stress 24h|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 ctrl 97hpf#2 lc 24h#2 lc 24h#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T174_good_2.fq.gz Zebrafish_N082-01-T174_good_1.fq.gz fastq fastq 8594096990.0 28965068.0 Zebrafish N082 01 T174 good 1.fq.gz 0:148.35 1:148.35 A:2196316723;C:2104410238;G:2114879320;T:2178397090;N:93619 148 148     2196316723 2104410238 2114879320 2178397090 93619 SRX8705678 SRS6982488 SRA1097128 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94907 0.94954 0.07407 0.07391 0.68211 0.68103 0.46688 0.46602 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-10 Larval Larval Trunk Surface Structure
60163 60163 SRR12191840 SRX8705677 SRS6982487 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh replicate #1 lc 24h#1 lc 24h#1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:lethal cold stress 24h|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 ctrl 97hpf#1 lc 24h#1 lc 24h#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T173_good_1.fq.gz Zebrafish_N082-01-T173_good_2.fq.gz fastq fastq 8305088740.0 27997786.0 Zebrafish N082 01 T173 good 1.fq.gz 0:148.32 1:148.32 A:2135411627;C:2023186538;G:2029512813;T:2116886895;N:90867 148 148     2135411627 2023186538 2029512813 2116886895 90867 SRX8705677 SRS6982487 SRA1097128 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94913 0.94986 0.08265 0.08233 0.67862 0.67754 0.46912 0.47096 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-10 Larval Larval Trunk Surface Structure
60164 60164 SRR12185264 SRX8699812 SRS6977660 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 1h recovery at normal temperature replicate #3 re 1h#3 re 1h#3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 1h|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 ctrl 97hpf#3 re 1h#3 re 1h#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T103_good_2.fq.gz Zebrafish_N082-01-T103_good_1.fq.gz fastq fastq 9268288718.0 31090829.0 Zebrafish N082 01 T103 good 1.fq.gz 0:149.05 1:149.05 A:2352761773;C:2286212082;G:2297633242;T:2331672593;N:9028 149 149     2352761773 2286212082 2297633242 2331672593 9028 SRX8699812 SRS6977660 SRA1096786 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94834 0.95086 0.06189 0.06211 0.66918 0.66839 0.45877 0.46583 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-10 Larval Larval Trunk Surface Structure
60165 60165 SRR12185265 SRX8699811 SRS6977659 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 1h recovery at normal temperature replicate #2 re 1h#2 re 1h#2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 1h|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 ctrl 97hpf#2 re 1h#2 re 1h#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T102_good_1.fq.gz Zebrafish_N082-01-T102_good_2.fq.gz fastq fastq 10291789534.0 34515378.0 Zebrafish N082 01 T102 good 1.fq.gz 0:149.09 1:149.09 A:2622881654;C:2528940070;G:2540934572;T:2599023030;N:10208 149 149     2622881654 2528940070 2540934572 2599023030 10208 SRX8699811 SRS6977659 SRA1096786 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94991 0.95114 0.06338 0.06422 0.66884 0.6686 0.4615 0.45962 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-10 Larval Larval Trunk Surface Structure
60166 60166 SRR12185266 SRX8699810 SRS6977658 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh followed by 1h recovery at normal temperature replicate #1 re 1h#1 re 1h#1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:recovery 1h|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 ctrl 97hpf#1 re 1h#1 re 1h#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T101_good_1.fq.gz Zebrafish_N082-01-T101_good_2.fq.gz fastq fastq 7717856658.0 25883590.0 Zebrafish N082 01 T101 good 1.fq.gz 0:149.09 1:149.09 A:1952564085;C:1907899915;G:1920973821;T:1936411176;N:7661 149 149     1952564085 1907899915 1920973821 1936411176 7661 SRX8699810 SRS6977658 SRA1096786 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.95003 0.95187 0.06064 0.06115 0.66805 0.66758 0.46042 0.46086 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-10 Larval Larval Trunk Surface Structure
60167 60167 SRR12182181 SRX8696733 SRS6974623 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh replicate #3 lc 12h#3 lc 12h#3   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:lethal cold stress 12h|replicate:biological replicate 3|BioSampleModel:Model organism or animal                 ctrl 97hpf#3 lc 12h#3 lc 12h#3 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2102 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T97_good_1.fq.gz Zebrafish_N082-01-T97_good_2.fq.gz fastq fastq 10000493852.0 33512452.0 Zebrafish N082 01 T97 good 1.fq.gz 0:149.21 1:149.21 A:2550626200;C:2455040644;G:2471313138;T:2523503973;N:9897 149 149     2550626200 2455040644 2471313138 2523503973 9897 SRX8696733 SRS6974623 SRA1096713 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94567 0.94653 0.0732 0.07308 0.6745 0.67491 0.45441 0.45192 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-09 Larval Larval Trunk Surface Structure
60168 60168 SRR12182182 SRX8696732 SRS6974622 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh replicate #2 lc 12h#2 lc 12h#2   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:lethal cold stress 12h|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 ctrl 97hpf#2 lc 12h#2 lc 12h#2 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2101 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T96_good_2.fq.gz Zebrafish_N082-01-T96_good_1.fq.gz fastq fastq 9556118200.0 32085173.0 Zebrafish N082 01 T96 good 1.fq.gz 0:148.92 1:148.92 A:2432004886;C:2349392247;G:2365447039;T:2409264784;N:9244 148 148     2432004886 2349392247 2365447039 2409264784 9244 SRX8696732 SRS6974622 SRA1096713 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94673 0.9471 0.07264 0.07262 0.67604 0.67623 0.4676 0.46887 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-09 Larval Larval Trunk Surface Structure
60169 60169 SRR12182183 SRX8696731 SRS6974621 SRP270158 PRJNA644214 Danio rerio Transcriptome under lethal cold stress PRJNA644214 Transcriptome Analysis The transcriptional regulations of fish upon a lethal cold stress and during the following rewarming are not well known. The purpose of this study is to characterize the gene expression dynamics of zebrafish larvae exposed to lethal cold stress and subsequent rewarming. Our data defined the survival and death pathways determining the survival of fish from the cold induced cellular or tissue damage. Modulating the activities of these pathways may enhance cold tolerance of the cold sensitive farmed fishes.     Zebrafish larvae exposed to lethal cold stress for xxxh replicate #1 lc 12h#1 lc 12h#1   strain:AB|dev stage:Larvae|sex:not applicable|tissue:Whole body|biomaterial provider:Zongbin Cui No. 7 Donghu South Road Wuchang District Wuhan Hubei Province China|treatment:lethal cold stress 12h|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 ctrl 97hpf#1 lc 12h#1 lc 12h#1 The RNA sample was sent to Biomarker Technologies http://www.biomarker.com.cn for library construction and RNA sequencing. Briefly mRNA molecules were enriched using Oligo dT magnetic beads and randomly fragmented. First strand cDNA synthesis was performed using random hexamers. Second strand cDNAs were synthesized by adding dNTPs RNase and DNA polymerase. The double stranded cDNAs were purified using AMPure XP beads. post end filling A tailing and sequencing adaptor ligation cDNA fragments of desired size were selected using AMPure XP beads. Finally the sequencing library was generated by PCR amplification. Library quantification was performed using a Qubit 2.0 and the insert size of library was analyzed by an Agilent 2100 Bioanalyzer system.     RNA-Seq TRANSCRIPTOMIC PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP270158     Zebrafish_N082-01-T95_good_1.fq.gz Zebrafish_N082-01-T95_good_2.fq.gz fastq fastq 11511360014.0 38631361.0 Zebrafish N082 01 T95 good 1.fq.gz 0:148.99 1:148.99 A:2914647594;C:2846271092;G:2861624774;T:2888804531;N:12023 148 148     2914647594 2846271092 2861624774 2888804531 12023 SRX8696731 SRS6974621 SRA1096713 Chinese Academy of Sciences|Institute of Hydrobiology Chinese Academy of Sciences 2 0.94679 0.9488 0.06686 0.0673 0.67746 0.6773 0.44988 0.4488 150 150 B B biological fallback assumption illumina novaseq_era unknown random_priming unknown bulk unknown unknown   China 2020-07-09 Larval Larval Trunk Surface Structure

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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");;