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run_metadata

99 rows where devstage_curation = "Larval" and experiment.library_selection = "RT-PCR"

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tissue_curation 6

technology 2

experiment.library_source 2

experiment.library_layout 2

experiment.platform 1

experiment.library_strategy 1

experiment.library_selection 1

  • RT-PCR · 99 ✖

devstage_curation_coarse 1

devstage_curation 1

  • Larval · 99 ✖
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
31884 31884 SRR28747851 SRX24313483 SRS21075233 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish control sample3   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish control 3 Ctrl 3 Ctrl 3 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     Ctrl-3_S26_L004_R2_001.fastq.gz Ctrl-3_S26_L004_R1_001.fastq.gz fastq fastq 6658139400.0 22193798.0 Ctrl 3 S26 L004 R1 001.fastq.gz 0:150 1:150 A:1953050910;C:1380426193;G:1413459206;T:1911166654;N:36437 150 150     1953050910 1380426193 1413459206 1911166654 36437 SRX24313483 SRS21075233 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.94694 0.94695 0.14305 0.14206 0.70412 0.70473 0.59878 0.59922 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31885 31885 SRR28747852 SRX24313482 SRS21075231 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish control sample2   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish control 2 Ctrl 2 Ctrl 2 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     Ctrl-2_S25_L004_R1_001.fastq.gz Ctrl-2_S25_L004_R2_001.fastq.gz fastq fastq 7515161100.0 25050537.0 Ctrl 2 S25 L004 R1 001.fastq.gz 0:150 1:150 A:2218032458;C:1545198589;G:1580900913;T:2170988635;N:40505 150 150     2218032458 1545198589 1580900913 2170988635 40505 SRX24313482 SRS21075231 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.94205 0.94032 0.15138 0.15085 0.69578 0.69645 0.5641 0.56481 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31886 31886 SRR28747853 SRX24313481 SRS21075234 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish control sample1   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish control 1 Ctrl 1 Ctrl 1 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     Ctrl-1_S24_L004_R1_001.fastq.gz Ctrl-1_S24_L004_R2_001.fastq.gz fastq fastq 9747041100.0 32490137.0 Ctrl 1 S24 L004 R1 001.fastq.gz 0:150 1:150 A:2863031605;C:2014131410;G:2067943208;T:2801881561;N:53316 150 150     2863031605 2014131410 2067943208 2801881561 53316 SRX24313481 SRS21075234 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.94378 0.94419 0.14935 0.14934 0.70749 0.7069 0.60161 0.59912 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31887 31887 SRR28747854 SRX24313480 SRS21075232 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish 4 octyl itaconate sample3   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish 4 octyl itaconate 3 4OI 3 4OI 3 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     4OI-3_S23_L004_R1_001.fastq.gz 4OI-3_S23_L004_R2_001.fastq.gz fastq fastq 8273990400.0 27579968.0 4OI 3 S23 L004 R1 001.fastq.gz 0:150 1:150 A:2162937415;C:1975194532;G:2012089890;T:2123723196;N:45367 150 150     2162937415 1975194532 2012089890 2123723196 45367 SRX24313480 SRS21075232 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.96535 0.96542 0.03083 0.03097 0.71279 0.71295 0.48276 0.47927 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31888 31888 SRR28747855 SRX24313479 SRS21075230 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish 4 octyl itaconate sample2   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish 4 octyl itaconate 2 4OI 2 4OI 2 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     4OI-2_S28_L003_R1_001.fastq.gz 4OI-2_S28_L003_R2_001.fastq.gz fastq fastq 6579714300.0 21932381.0 4OI 2 S28 L003 R1 001.fastq.gz 0:150 1:150 A:1710345718;C:1580260893;G:1608081826;T:1680921918;N:103945 150 150     1710345718 1580260893 1608081826 1680921918 103945 SRX24313479 SRS21075230 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.96511 0.96418 0.03843 0.0384 0.70179 0.7027 0.49174 0.5066 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
31889 31889 SRR28747856 SRX24313478 SRS21075229 SRP502930 PRJNA1102048 Danio rerio Raw sequence reads PRJNA1102048 Whole Genome Sequencing This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA seq analysis. At 5dpf Larvae treated with 4 octyl itaconate was preformed to subsequent transcriptomic analysis.       Model organism or animal sample from Danio rerio Zebrafish 4 octyl itaconate sample1   strain:TgBrn3C:mGFP|age:5dpf|collection date:2022 09 25|geo loc name:China|sex:pooled male and female|tissue:larvae|BioSampleModel:Model organism or animal                 Zebrafish 4 octyl itaconate 1 4OI 1 4OI 1 DNA barcode     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP502930     4OI-1_S27_L003_R1_001.fastq.gz 4OI-1_S27_L003_R2_001.fastq.gz fastq fastq 7099570500.0 23665235.0 4OI 1 S27 L003 R1 001.fastq.gz 0:150 1:150 A:1858012411;C:1693592911;G:1723374425;T:1824476953;N:113800 150 150     1858012411 1693592911 1723374425 1824476953 113800 SRX24313478 SRS21075229 SRA1849567 Nantong University|Institute of Special Environmental Medicine Nantong University 2 0.96619 0.96559 0.04154 0.04152 0.70386 0.70412 0.48321 0.49372 150 150 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-04-19 Larval Larval Whole Organism All anatomical structures
32617 32617 SRR29366294 SRX24880743 SRS21589520 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs4   strain:TU|isolate:NPs4|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs4 NPs4 A total amount of 9 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0022_good_1.fq.gz Unknown_BO623-04T0022_good_2.fq.gz fastq fastq 6748273836.0 22592809.0 Unknown BO623 04T0022 good 1.fq.gz 0:149.35 1:149.35 A:1774719919;C:1597377190;G:1614927098;T:1761071358;N:178271 149 149     1774719919 1597377190 1614927098 1761071358 178271 SRX24880743 SRS21589520 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32618 32618 SRR29366295 SRX24880742 SRS21589518 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs3   strain:TU|isolate:NPs3|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs3 NPs3 A total amount of 8 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0021_good_1.fq.gz Unknown_BO623-04T0021_good_2.fq.gz fastq fastq 6529485490.0 21847936.0 Unknown BO623 04T0021 good 1.fq.gz 0:149.43 1:149.43 A:1717039978;C:1547743896;G:1563982349;T:1700522682;N:196585 149 149     1717039978 1547743896 1563982349 1700522682 196585 SRX24880742 SRS21589518 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32619 32619 SRR29366296 SRX24880741 SRS21589519 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs2   strain:TU|isolate:NPs2|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs2 NPs2 A total amount of 7 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0020_good_1.fq.gz Unknown_BO623-04T0020_good_2.fq.gz fastq fastq 6699049910.0 22407080.0 Unknown BO623 04T0020 good 1.fq.gz 0:149.49 1:149.49 A:1761959579;C:1586799482;G:1603631340;T:1746520369;N:139140 149 149     1761959579 1586799482 1603631340 1746520369 139140 SRX24880741 SRS21589519 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32620 32620 SRR29366297 SRX24880740 SRS21589517 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs1   strain:TU|isolate:NPs1|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs1 NPs1 A total amount of 6 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0019_good_1.fq.gz Unknown_BO623-04T0019_good_2.fq.gz fastq fastq 6132468788.0 20516184.0 Unknown BO623 04T0019 good 1.fq.gz 0:149.45 1:149.45 A:1607332987;C:1458658424;G:1471957341;T:1594421337;N:98699 149 149     1607332987 1458658424 1471957341 1594421337 98699 SRX24880740 SRS21589517 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32621 32621 SRR29366298 SRX24880739 SRS21589516 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C6   strain:TU|isolate:Control6|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C6 C6 A total amount of 5 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0018_good_1.fq.gz Unknown_BO623-04T0018_good_2.fq.gz fastq fastq 5940082248.0 19857041.0 Unknown BO623 04T0018 good 1.fq.gz 0:149.57 1:149.57 A:1533707674;C:1435538751;G:1452812826;T:1517833025;N:189972 149 149     1533707674 1435538751 1452812826 1517833025 189972 SRX24880739 SRS21589516 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32622 32622 SRR29366299 SRX24880738 SRS21589515 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C5   strain:TU|isolate:Control5|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C5 C5 A total amount of 4 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0017_good_1.fq.gz Unknown_BO623-04T0017_good_2.fq.gz fastq fastq 6758002932.0 22599590.0 Unknown BO623 04T0017 good 1.fq.gz 0:149.52 1:149.52 A:1739766340;C:1637642157;G:1652002401;T:1728330255;N:261779 149 149     1739766340 1637642157 1652002401 1728330255 261779 SRX24880738 SRS21589515 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32623 32623 SRR29366300 SRX24880737 SRS21589514 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C4   strain:TU|isolate:Control4|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C4 C4 A total amount of 3 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0016_good_1.fq.gz Unknown_BO623-04T0016_good_2.fq.gz fastq fastq 6210972784.0 20767744.0 Unknown BO623 04T0016 good 1.fq.gz 0:149.53 1:149.53 A:1591917700;C:1506245368;G:1529628371;T:1583090947;N:90398 149 149     1591917700 1506245368 1529628371 1583090947 90398 SRX24880737 SRS21589514 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32624 32624 SRR29366301 SRX24880736 SRS21589513 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C3   strain:TU|isolate:Control3|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C3 C3 A total amount of 2 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0015_good_1.fq.gz Unknown_BO623-04T0015_good_2.fq.gz fastq fastq 6666249022.0 22284306.0 Unknown BO623 04T0015 good 1.fq.gz 0:149.57 1:149.57 A:1722337869;C:1610144787;G:1630507947;T:1703082771;N:175648 149 149     1722337869 1610144787 1630507947 1703082771 175648 SRX24880736 SRS21589513 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32625 32625 SRR29366302 SRX24880735 SRS21589512 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs6   strain:TU|isolate:NPs6|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs6 NPs6 A total amount of11 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0024_good_1.fq.gz Unknown_BO623-04T0024_good_2.fq.gz fastq fastq 6819262402.0 22797722.0 Unknown BO623 04T0024 good 1.fq.gz 0:149.56 1:149.56 A:1781861689;C:1629655448;G:1645382478;T:1762184452;N:178335 149 149     1781861689 1629655448 1645382478 1762184452 178335 SRX24880735 SRS21589512 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32626 32626 SRR29366303 SRX24880734 SRS21589511 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         NPs5   strain:TU|isolate:NPs5|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae NPs5 NPs5 A total amount of10 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0023_good_1.fq.gz Unknown_BO623-04T0023_good_2.fq.gz fastq fastq 6773730348.0 22673915.0 Unknown BO623 04T0023 good 1.fq.gz 0:149.37 1:149.37 A:1779182337;C:1607164031;G:1624141377;T:1763062617;N:179986 149 149     1779182337 1607164031 1624141377 1763062617 179986 SRX24880734 SRS21589511 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32627 32627 SRR29366304 SRX24880733 SRS21589509 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C2   strain:TU|isolate:Control2|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C2 C2 A total amount of 1 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following manufacturers recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads.First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3 ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. The library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 l USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37C for 15 min followed by 5 min at 95C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0014_good_1.fq.gz Unknown_BO623-04T0014_good_2.fq.gz fastq fastq 6805354296.0 22755187.0 Unknown BO623 04T0014 good 1.fq.gz 0:149.53 1:149.53 A:1742825793;C:1651738009;G:1677448209;T:1733168084;N:174201 149 149     1742825793 1651738009 1677448209 1733168084 174201 SRX24880733 SRS21589509 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
32628 32628 SRR29366305 SRX24880732 SRS21589510 SRP513315 PRJNA1122875 Transcriptome of zebrafish Danio rerio larvae exposed to MPs at xxx dpf PRJNA1122875 Other This study aims to figure out the NPs toxicity on zebrafish at early stages especially on visual system development.         C1   strain:TU|isolate:Control1|age:5dpf|collection date:2023 07 30|geo loc name:China:Zhejiang|sex:pooled male and female|tissue:the front part of larvae|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish larvae C1 C1 A total amount of 0 g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual mode mRNA Library Prep Kit for Illumina Yeasen Biotechnology Shanghai Co. Ltd. following x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000 x0000…     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP513315     Unknown_BO623-04T0013_good_1.fq.gz Unknown_BO623-04T0013_good_2.fq.gz fastq fastq 6546144006.0 21896126.0 Unknown BO623 04T0013 good 1.fq.gz 0:149.48 1:149.48 A:1688579059;C:1582023304;G:1598552166;T:1676633897;N:355580 149 149     1688579059 1582023304 1598552166 1676633897 355580 SRX24880732 SRS21589510 SRA1896007 Zhejiang University|College of Animal Science Zhejiang University                       B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2024-06-11 Larval Larval Whole Organism All anatomical structures
33369 33369 SRR30159204 SRX25626516 SRS22271512 SRP524652 PRJNA1145276 The RNA sequence analysis post lossing tango6 PRJNA1145276 Other To detect RNA expression level difference post lost of TANGO6         Mutant 2   strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.8 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal                 Mutant 2 Li lab 003 4 Li lab 003 4 RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 6 g of total RNA was used for construction of sequencing libraries.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP524652     7c166f592635e7a5f904d56dd661e1cc mut-2_1.fq.gz.gz 3adc1733ac4cb77beca49461cb17544b mut-2_2.fq.gz.gz fastq fastq 5518961400.0 18396538.0 3adc1733ac4cb77beca49461cb17544b mut 2 2.fq.gz.gz 0:150 1:150 A:1469924277;C:1285547670;G:1307420673;T:1455990444;N:78336 150 150     1469924277 1285547670 1307420673 1455990444 78336 SRX25626516 SRS22271512 SRA1941919 Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences 2 0.96085 0.95919 0.05548 0.05519 0.7207 0.72178 0.47759 0.47549 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-07 Larval Larval Undetermined Undetermined
33370 33370 SRR30159205 SRX25626515 SRS22271511 SRP524652 PRJNA1145276 The RNA sequence analysis post lossing tango6 PRJNA1145276 Other To detect RNA expression level difference post lost of TANGO6         Mutant 1   strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.7 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal                 Mutant 1 Li lab 003 3 Li lab 003 3 RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 5 g of total RNA was used for construction of sequencing libraries.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP524652     39cb7947119cec5afac3df66c0ae0048 mut-1_1.fq.gz.gz 1bfc59902758bb1cbf8eb4549d3375fd mut-1_2.fq.gz.gz fastq fastq 5947120500.0 19823735.0 1bfc59902758bb1cbf8eb4549d3375fd mut 1 2.fq.gz.gz 0:150 1:150 A:1567673549;C:1401761128;G:1423907629;T:1553701047;N:77147 150 150     1567673549 1401761128 1423907629 1553701047 77147 SRX25626515 SRS22271511 SRA1941919 Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences 2 0.96303 0.96203 0.05003 0.04984 0.72271 0.72299 0.47608 0.47831 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-07 Larval Larval Undetermined Undetermined
33371 33371 SRR30159206 SRX25626514 SRS22271510 SRP524652 PRJNA1145276 The RNA sequence analysis post lossing tango6 PRJNA1145276 Other To detect RNA expression level difference post lost of TANGO6         Wild type 2   strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.6 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal                 Wild type 2 Li lab 003 2 Li lab 003 2 RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 4 g of total RNA was used for construction of sequencing libraries.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP524652     4376e7007befe0cf23ffa7f9dd62512c sib-3_1.fq.gz.gz da4d46fd26ca22e90409489640659b1c sib-3_2.fq.gz.gz fastq fastq 6113935200.0 20379784.0 4376e7007befe0cf23ffa7f9dd62512c sib 3 1.fq.gz.gz 0:150 1:150 A:1609711214;C:1443384557;G:1461871812;T:1598876167;N:91450 150 150     1609711214 1443384557 1461871812 1598876167 91450 SRX25626514 SRS22271510 SRA1941919 Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences 2 0.95947 0.9591 0.04902 0.0492 0.71707 0.71796 0.46871 0.4604 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-07 Larval Larval Undetermined Undetermined
33372 33372 SRR30159207 SRX25626513 SRS22271509 SRP524652 PRJNA1145276 The RNA sequence analysis post lossing tango6 PRJNA1145276 Other To detect RNA expression level difference post lost of TANGO6         Wild type 1   strain:AB|isolate:trizol extraction|breed:standard breed|cultivar:not collected|ecotype:not collected|age:not collected|dev stage:3.5 dpf|collection date:2024 02 04|geo loc name:not collected|sex:not collected|tissue:CHT|BioSampleModel:Model organism or animal                 Wild type 1 Li lab 003 1 Li lab 003 1 RNA was harvested using RNeasy Mini Kit Qiagen PureLink RNA Mini Kit Thermo. 1.5 3 g of total RNA was used for construction of sequencing libraries.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP524652     319b2e8b61305a8937eb903a7a20a2e7 sib-2_1.fq.gz.gz 4a84982431b5360126f279ceabf00548 sib-2_2.fq.gz.gz fastq fastq 6351813000.0 21172710.0 319b2e8b61305a8937eb903a7a20a2e7 sib 2 1.fq.gz.gz 0:150 1:150 A:1674596701;C:1497102731;G:1525030471;T:1654985592;N:97505 150 150     1674596701 1497102731 1525030471 1654985592 97505 SRX25626513 SRS22271509 SRA1941919 Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences|Research center of Stem cells and Ageing Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences 2 0.96469 0.96334 0.04679 0.04633 0.73119 0.73198 0.47359 0.47265 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2024-08-07 Larval Larval Undetermined Undetermined
36600 36600 SRR633516 SRX209919 SRS379598 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae maintained at control conditiion replicate 1 ck1                     dataset of ck1 Seq1 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563     ck1_run2_R1.fastq.gz ck1_run2_R2.fastq.gz fastq fastq 1425533040.0 19799070.0 Run 1 0:36 1:36 A:346892627;C:359716472;G:360029628;T:357662709;N:1231604 36 36     346892627 359716472 360029628 357662709 1231604 SRX209919 SRS379598 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.93467 0.92945 0.06912 0.06892 0.67101 0.67233 0.45594 0.45635 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2012-12-16 Larval Larval Undetermined Undetermined
36601 36601 SRR633554 SRX210639 SRS379606 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae exposed to hypoxia stress replicate 3 hypo3                     dataset for sample hypo3 Seq9 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563         1048140792.0 14557511.0 hypo3 run1 0:36 1:36 A:259618733;C:259785246;G:262230196;T:266244448;N:262169 36 36     259618733 259785246 262230196 266244448 262169 SRX210639 SRS379606 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.93986 0.93562 0.06965 0.06854 0.67006 0.67131 0.43686 0.45545 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2012-12-18 Larval Larval Undetermined Undetermined
36602 36602 SRR633555 SRX210639 SRS379606 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae exposed to hypoxia stress replicate 3 hypo3                     dataset for sample hypo3 Seq9 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563     hypo3_run2_R2.fastq.gz fastq 1000001376.0 13888908.0 hypo3 run2 0:36 1:36 A:246155193;C:248766521;G:251127505;T:252483880;N:1468277 36 36     246155193 248766521 251127505 252483880 1468277 SRX210639 SRS379606 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.93954 0.93167 0.06689 0.06675 0.67322 0.6748 0.46287 0.4641 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2013-12-13 Larval Larval Undetermined Undetermined
36603 36603 SRR633552 SRX210638 SRS379605 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae exposed to hypoxia stress replicate 2 hypo2                     dataset for sample hypo2 Seq8 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563         944842752.0 13122816.0 hypo2 run1 0:36 1:36 A:230936699;C:236712021;G:238060792;T:238878037;N:255203 36 36     230936699 236712021 238060792 238878037 255203 SRX210638 SRS379605 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.93909 0.93309 0.07087 0.07105 0.6672 0.66813 0.46107 0.45873 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2012-12-18 Larval Larval Undetermined Undetermined
36604 36604 SRR633553 SRX210638 SRS379605 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae exposed to hypoxia stress replicate 2 hypo2                     dataset for sample hypo2 Seq8 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563     hypo2_run2_R2.fastq.gz fastq 988361568.0 13727244.0 hypo2 run2 0:36 1:36 A:240212534;C:248205313;G:250004116;T:248599375;N:1340230 36 36     240212534 248205313 250004116 248599375 1340230 SRX210638 SRS379605 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.94029 0.93226 0.07174 0.0704 0.67129 0.67142 0.44913 0.45448 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2013-12-13 Larval Larval Undetermined Undetermined
36605 36605 SRR633550 SRX210637 SRS379604 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae exposed to hypoxia stress replicate 1 hypo1                     dataset for sample hypo1 Seq7 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563         1111534488.0 15437979.0 hypo1 run1 0:36 1:36 A:273016370;C:277718934;G:279150260;T:281380668;N:268256 36 36     273016370 277718934 279150260 281380668 268256 SRX210637 SRS379604 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.93448 0.92737 0.07734 0.077 0.66886 0.67012 0.45226 0.45356 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2012-12-17 Larval Larval Undetermined Undetermined
36606 36606 SRR633551 SRX210637 SRS379604 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae exposed to hypoxia stress replicate 1 hypo1                     dataset for sample hypo1 Seq7 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563     hypo1_run2_R2.fastq.gz fastq 1086628536.0 15092063.0 hypo run2 0:36 1:36 A:265451380;C:271989493;G:274094744;T:273520855;N:1572064 36 36     265451380 271989493 274094744 273520855 1572064 SRX210637 SRS379604 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.9313 0.92722 0.07613 0.07533 0.67511 0.67468 0.45532 0.4554 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2012-12-17 Larval Larval Undetermined Undetermined
36607 36607 SRR633548 SRX210636 SRS379603 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae exposed to cold stress replicate 3 cold3                     dataset for sample cold3 Seq6 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563     cold3_run1_R2.fastq.gz fastq 856370016.0 11894028.0 cold3 run1 0:36 1:36 A:203894018;C:218965032;G:223278100;T:210022674;N:210192 36 36     203894018 218965032 223278100 210022674 210192 SRX210636 SRS379603 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.9356 0.93083 0.06354 0.06342 0.67495 0.67659 0.46514 0.46632 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2013-12-13 Larval Larval Undetermined Undetermined
36608 36608 SRR633549 SRX210636 SRS379603 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae exposed to cold stress replicate 3 cold3                     dataset for sample cold3 Seq6 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563         912477384.0 12673297.0 cold3 run2 0:36 1:36 A:216126045;C:233918163;G:238615002;T:222532152;N:1286022 36 36     216126045 233918163 238615002 222532152 1286022 SRX210636 SRS379603 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.93707 0.93034 0.06328 0.06231 0.68199 0.68154 0.45852 0.45712 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2012-12-17 Larval Larval Undetermined Undetermined
36609 36609 SRR633546 SRX210635 SRS379602 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae exposed to cold stress replicate 2 cold2                     dataset for sample cold2 Seq5 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563     cold2_run1_R2.fastq.gz fastq 758704104.0 10537557.0 cold2 run1 0:36 1:36 A:183694352;C:191591559;G:194571241;T:188644215;N:202737 36 36     183694352 191591559 194571241 188644215 202737 SRX210635 SRS379602 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.9355 0.93037 0.07579 0.07546 0.67758 0.67799 0.46336 0.4537 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2012-12-17 Larval Larval Undetermined Undetermined
36610 36610 SRR633547 SRX210635 SRS379602 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae exposed to cold stress replicate 2 cold2                     dataset for sample cold2 Seq5 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563         758269944.0 10531527.0 cold2 run2 0:36 1:36 A:182477606;C:192044319;G:195270817;T:187486180;N:991022 36 36     182477606 192044319 195270817 187486180 991022 SRX210635 SRS379602 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.93526 0.92936 0.07437 0.07319 0.68252 0.68243 0.45977 0.45219 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2012-12-17 Larval Larval Undetermined Undetermined
36611 36611 SRR633544 SRX210634 SRS379601 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae exposed to cold stress replicate 1 cold1                     dataset for sample cold1 Seq4 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563         939174120.0 13044085.0 cold1 run1 0:36 1:36 A:229908173;C:234619234;G:239161528;T:235262399;N:222786 36 36     229908173 234619234 239161528 235262399 222786 SRX210634 SRS379601 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.92711 0.91958 0.08119 0.08052 0.67032 0.67249 0.4669 0.4661 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2012-12-17 Larval Larval Undetermined Undetermined
36612 36612 SRR633545 SRX210634 SRS379601 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae exposed to cold stress replicate 1 cold1                     dataset for sample cold1 Seq4 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563     cold1_run2_R2.fastq.gz fastq 969327360.0 13462880.0 cold1 run2 0:36 1:36 A:236017916;C:242777395;G:247690199;T:241486770;N:1355080 36 36     236017916 242777395 247690199 241486770 1355080 SRX210634 SRS379601 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.92225 0.91649 0.08088 0.07942 0.67811 0.67819 0.47395 0.47096 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2013-12-13 Larval Larval Undetermined Undetermined
36613 36613 SRR633542 SRX210633 SRS379600 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae maintained at control condition replicate 3 ck3                     dataset for sample ck3 Seq3 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563         712122912.0 9890596.0 ck3 run1 0:36 1:36 A:173202209;C:178330394;G:181430842;T:178980355;N:179112 36 36     173202209 178330394 181430842 178980355 179112 SRX210633 SRS379600 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.93432 0.92622 0.07444 0.07347 0.66267 0.66381 0.45819 0.45458 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2012-12-17 Larval Larval Undetermined Undetermined
36614 36614 SRR633543 SRX210633 SRS379600 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae maintained at control condition replicate 3 ck3                     dataset for sample ck3 Seq3 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563         690216696.0 9586343.0 ck3 run2 0:36 1:36 A:166782468;C:173577192;G:176360566;T:172494787;N:1001683 36 36     166782468 173577192 176360566 172494787 1001683 SRX210633 SRS379600 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.93384 0.92481 0.07221 0.07087 0.66813 0.6692 0.45481 0.4573 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2012-12-16 Larval Larval Undetermined Undetermined
36615 36615 SRR633540 SRX210632 SRS379599 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae maintained at control condition replicate 2 ck2                     dataset for sample ck2 Seq2 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563     ck2_run1_R1.fastq.gz ck2_run1_R2.fastq.gz fastq fastq 893329776.0 12407358.0 run1 0:36 1:36 A:218731725;C:223935822;G:225438843;T:224982678;N:240708 36 36     218731725 223935822 225438843 224982678 240708 SRX210632 SRS379599 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.92555 0.92021 0.07993 0.08001 0.6631 0.66358 0.46925 0.46964 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2013-12-13 Larval Larval Undetermined Undetermined
36616 36616 SRR633541 SRX210632 SRS379599 SRP017563 PRJNA183864 Zebrafish larvae exposed to cold or hypoxia stress PRJNA183864 Other To investigate the transcriptional regulation in zebrafish larvae exposed environmental stresses larvae at xxxhpf were exposed to cold stress 16 Celsius degree or hypoxia 5% O2 for 24h and the controls were maintained at 28 Celsius degree and atmosphere O2 concentration. post environmental exposure RNAs were extracted and subjected to RNA sequencing using Illumina genome analyzer IIx platform.     1 zebrafish larvae maintained at control condition replicate 2 ck2                     dataset for sample ck2 Seq2 1 1     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina Genome Analyzer IIx <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>72</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>37</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP017563         886248648.0 12309009.0 run2 0:36 1:36 A:215735507;C:222732158;G:224616280;T:221967000;N:1197703 36 36     215735507 222732158 224616280 221967000 1197703 SRX210632 SRS379599 SRA062881 Institute of Hydrobiology, Chinese Academy of Scie|Environmental genomics group Institute of Hydrobiology, Chinese Academy of Sciences 2 0.92626 0.91948 0.07987 0.07869 0.66785 0.66778 0.46701 0.4675 36 36 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   China 2012-12-16 Larval Larval Undetermined Undetermined
45033 45033 SRR6466457 SRX3556410 SRS2829758 SRP128941 PRJNA428924 Danio rerio breed:TU Transcriptome or Gene expression PRJNA428924 Transcriptome Analysis In order to know about more basic knowledge of none/less gut adhesive strain L. casei BL23 induce on the developmental profile and immunity education in zebrafish     pooled of 30 whole body larvae fish at 14 dpf old.   Control 14   breed:TU|age:14 dpf|sex:pooled male and female|tissue:whole body|treatment:Control|BioSampleModel:Model organism or animal                 RNA seq of zebrafish larvae with or without xxx administration Ctl 14 Ctl 14 Total RNA were isolated from pooled samples of larvae whole body or juvenile s intestines with TRIzol Tian Gen Beijing China following the manufacturer s specifications. The RNA was treated with amplification grade DNase I 1 U/ g RNA; Invitrogen USA. RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the RNA RIN values were bigger than 9.5 as analyzed by Bioanalyzer 2100 system. For mRNAseq equal volume and amount 1 g of total RNA from 4 sample pools of each treatment group were mixed as a sequencing sample.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP128941     ZF_CK_1.fq.gz ZF_CK_2.fq.gz fastq fastq 3194379750.0 12777519.0 ZF CK 1.fq.gz 0:125 1:125 A:843962375;C:752856573;G:753886188;T:843555573;N:119041 125 125     843962375 752856573 753886188 843555573 119041 SRX3556410 SRS2829758 SRA646164 Chinese Academy of Agricultural Sciences|Key Laboratory for Feed Biotechnology of the Minis Chinese Academy of Agricultural Sciences 2 0.94377 0.94754 0.06883 0.06783 0.67442 0.67844 0.46844 0.472 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2018-01-12 Larval Larval Trunk Surface Structure
45034 45034 SRR6466458 SRX3556409 SRS2829757 SRP128941 PRJNA428924 Danio rerio breed:TU Transcriptome or Gene expression PRJNA428924 Transcriptome Analysis In order to know about more basic knowledge of none/less gut adhesive strain L. casei BL23 induce on the developmental profile and immunity education in zebrafish     pooled of 30 larvae of fish at 14 dpf with L. casei BL23 administration   BL23 14   breed:TU|age:14 dpf|sex:pooled male and female|tissue:whole body|treatment:BL23 administration|BioSampleModel:Model organism or animal                 RNA seq of zebrafish larvae with or without xxx administration BL23 14 BL23 14 Total RNA were isolated from pooled samples of larvae whole body or juvenile s intestines with TRIzol Tian Gen Beijing China following the manufacturer s specifications. The RNA was treated with amplification grade DNase I 1 U/ g RNA; Invitrogen USA. RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer Life Technologies CA USA. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system Agilent Technologies CA USA. All the RNA RIN values were bigger than 9.5 as analyzed by Bioanalyzer 2100 system. For mRNAseq equal volume and amount 1 g of total RNA from 4 sample pools of each treatment group were mixed as a sequencing sample.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2000   SRP128941     ZF_BL23_1.fq.gz ZF_BL23_2.fq.gz fastq fastq 3720774000.0 14883096.0 ZF BL23 2.fq.gz 0:125 1:125 A:974128380;C:885422072;G:887959104;T:973126100;N:138344 125 125     974128380 885422072 887959104 973126100 138344 SRX3556409 SRS2829757 SRA646164 Chinese Academy of Agricultural Sciences|Key Laboratory for Feed Biotechnology of the Minis Chinese Academy of Agricultural Sciences 2 0.94399 0.94862 0.0635 0.06328 0.66898 0.67243 0.48704 0.48297 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2018-01-12 Larval Larval Trunk Surface Structure
55465 55465 SRR10425371 SRX7121468 SRS5631400 SRP229414 PRJNA588649 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure PRJNA588649 Other           DBP 3   sample title for replicate:2 3|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal                 DBP 3 2 3 2 3 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP229414     160653A_DBP_3_S11_L001_R1_001.fastq.gz 160653A_DBP_3_S11_L001_R2_001.fastq.gz 160653A_DBP_3_S11_L002_R1_001.fastq.gz 160653A_DBP_3_S11_L002_R2_001.fastq.gz fastq fastq fastq fastq 4213944331.0 16837823.0 160653A DBP 3 S11 L001 R1 001.fastq.gz 0:125.11 1:125.16 A:1140267822;C:951856511;G:956555719;T:1143228000;N:22036279 125 125     1140267822 951856511 956555719 1143228000 22036279 SRX7121468 SRS5631400 SRA993820 Chinese academy of fishery sciences|fishery Resource and Environmental Research Center Chinese academy of fishery sciences 2 0.92075 0.92322 0.13421 0.13417 0.66884 0.67131 0.46585 0.45982 125 126 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2019-11-11 Larval Larval Embryo Imprecise All anatomical structures
55466 55466 SRR10425372 SRX7121467 SRS5631399 SRP229414 PRJNA588649 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure PRJNA588649 Other           DBP 2   sample title for replicate:2 2|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal                 DBP 2 2 2 2 2 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP229414     160653A_DBP_2_S23_L002_R1_001.fastq.gz 160653A_DBP_2_S23_L002_R2_001.fastq.gz fastq fastq 983641304.0 3925939.0 160653A DBP 2 S23 L002 R1 001.fastq.gz 0:125.26 1:125.29 A:263874385;C:226824475;G:226589811;T:265169405;N:1183228 125 125     263874385 226824475 226589811 265169405 1183228 SRX7121467 SRS5631399 SRA993820 Chinese academy of fishery sciences|fishery Resource and Environmental Research Center Chinese academy of fishery sciences 2 0.93403 0.93521 0.12516 0.12672 0.66596 0.66815 0.46015 0.46602 126 125 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2019-11-11 Larval Larval Embryo Imprecise All anatomical structures
55467 55467 SRR10425373 SRX7121466 SRS5631398 SRP229414 PRJNA588649 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure PRJNA588649 Other           DBP 1   sample title for replicate:2 1|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal                 DBP 1 2 1 2 1 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP229414     160653A_DBP_1_S10_L001_R1_001.fastq.gz 160653A_DBP_1_S10_L001_R2_001.fastq.gz 160653A_DBP_1_S10_L002_R1_001.fastq.gz 160653A_DBP_1_S10_L002_R2_001.fastq.gz fastq fastq fastq fastq 3902022384.0 15589553.0 160653A DBP 1 S10 L001 R1 001.fastq.gz 0:125.13 1:125.17 A:1041532695;C:895336677;G:897445748;T:1047319053;N:20388211 125 125     1041532695 895336677 897445748 1047319053 20388211 SRX7121466 SRS5631398 SRA993820 Chinese academy of fishery sciences|fishery Resource and Environmental Research Center Chinese academy of fishery sciences 2 0.92278 0.92593 0.12212 0.12242 0.66381 0.66653 0.46732 0.46157 126 126 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2019-11-11 Larval Larval Embryo Imprecise All anatomical structures
55468 55468 SRR10425374 SRX7121465 SRS5631397 SRP229414 PRJNA588649 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure PRJNA588649 Other           DEHP 3   sample title for replicate:1 3|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal                 DEHP 3 1 3 1 3 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP229414     160653A_DEHP_3_S9_L001_R1_001.fastq.gz 160653A_DEHP_3_S9_L001_R2_001.fastq.gz 160653A_DEHP_3_S9_L002_R1_001.fastq.gz 160653A_DEHP_3_S9_L002_R2_001.fastq.gz fastq fastq fastq fastq 3978190342.0 15890841.0 160653A DEHP 3 S9 L001 R1 001.fastq.gz 0:125.15 1:125.19 A:1057764550;C:917477196;G:923586377;T:1058742562;N:20619657 125 125     1057764550 917477196 923586377 1058742562 20619657 SRX7121465 SRS5631397 SRA993820 Chinese academy of fishery sciences|fishery Resource and Environmental Research Center Chinese academy of fishery sciences 2 0.92571 0.92902 0.11691 0.11736 0.67192 0.67383 0.46273 0.46475 125 126 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2019-11-11 Larval Larval Embryo Imprecise All anatomical structures
55469 55469 SRR10425375 SRX7121464 SRS5631396 SRP229414 PRJNA588649 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure PRJNA588649 Other           DEHP 2   sample title for replicate:1 2|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal                 DEHP 2 1 2 1 2 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP229414     160653A_DEHP_2_S22_L002_R1_001.fastq.gz 160653A_DEHP_2_S22_L002_R2_001.fastq.gz fastq fastq 925063432.0 3692039.0 160653A DEHP 2 S22 L002 R1 001.fastq.gz 0:125.26 1:125.30 A:247171641;C:214421668;G:215124515;T:247261313;N:1084295 125 125     247171641 214421668 215124515 247261313 1084295 SRX7121464 SRS5631396 SRA993820 Chinese academy of fishery sciences|fishery Resource and Environmental Research Center Chinese academy of fishery sciences 2 0.93712 0.93841 0.12004 0.12183 0.67231 0.6747 0.47057 0.46379 124 126 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2019-11-11 Larval Larval Embryo Imprecise All anatomical structures
55470 55470 SRR10425376 SRX7121463 SRS5631395 SRP229414 PRJNA588649 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure PRJNA588649 Other           DEHP 1   sample title for replicate:1 1|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal                 DEHP 1 1 1 1 1 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP229414     160653A_DEHP_1_S8_L001_R1_001.fastq.gz 160653A_DEHP_1_S8_L001_R2_001.fastq.gz 160653A_DEHP_1_S8_L002_R1_001.fastq.gz 160653A_DEHP_1_S8_L002_R2_001.fastq.gz fastq fastq fastq fastq 4181311851.0 16698140.0 160653A DEHP 1 S8 L001 R1 001.fastq.gz 0:125.19 1:125.22 A:1132179802;C:946301758;G:946478272;T:1135074674;N:21277345 125 125     1132179802 946301758 946478272 1135074674 21277345 SRX7121463 SRS5631395 SRA993820 Chinese academy of fishery sciences|fishery Resource and Environmental Research Center Chinese academy of fishery sciences 2 0.92101 0.92416 0.13798 0.13866 0.6678 0.66963 0.46137 0.46314 126 126 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2019-11-11 Larval Larval Embryo Imprecise All anatomical structures
55471 55471 SRR10425377 SRX7121462 SRS5631394 SRP229414 PRJNA588649 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure PRJNA588649 Other           con 3   sample title for replicate:0 3|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal                 con 3 0 3 0 3 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP229414     160653A_con_3_S7_L002_R2_001.fastq.gz 160653A_con_3_S7_L002_R1_001.fastq.gz 160653A_con_3_S7_L001_R2_001.fastq.gz 160653A_con_3_S7_L001_R1_001.fastq.gz fastq fastq fastq fastq 4645800774.0 18572727.0 160653A con 3 S7 L001 R1 001.fastq.gz 0:125.05 1:125.09 A:1251751873;C:1054269377;G:1062381476;T:1252233640;N:25164408 125 125     1251751873 1054269377 1062381476 1252233640 25164408 SRX7121462 SRS5631394 SRA993820 Chinese academy of fishery sciences|fishery Resource and Environmental Research Center Chinese academy of fishery sciences 2 0.9211 0.92397 0.13775 0.13782 0.6703 0.6728 0.46466 0.46374 125 125 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2019-11-11 Larval Larval Embryo Imprecise All anatomical structures
55472 55472 SRR10425378 SRX7121461 SRS5631393 SRP229414 PRJNA588649 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure PRJNA588649 Other           con 2   sample title for replicate:0 2|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal                 con 2 0 2 0 2 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP229414     160653A_con_2_S108_L008_R1_001.fastq.gz 160653A_con_2_S108_L008_R2_001.fastq.gz fastq fastq 752863995.0 3006358.0 160653A con 2 S108 L008 R1 001.fastq.gz 0:125.20 1:125.23 A:203171883;C:172318434;G:172771199;T:203551286;N:1051193 125 125     203171883 172318434 172771199 203551286 1051193 SRX7121461 SRS5631393 SRA993820 Chinese academy of fishery sciences|fishery Resource and Environmental Research Center Chinese academy of fishery sciences 2 0.93253 0.93349 0.13528 0.13652 0.66186 0.66665 0.46382 0.47405 126 126 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2019-11-11 Larval Larval Embryo Imprecise All anatomical structures
55473 55473 SRR10425379 SRX7121460 SRS5631392 SRP229414 PRJNA588649 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure PRJNA588649 Other           con 1   sample title for replicate:0 1|strain:AB|age:96hpf|sex:pooled male and female|tissue:embryo|BioSampleModel:Model organism or animal                 con 1 0 1 0 1 RNA sequencing for differential expression gene screening in zebrafish post DEHP and DBP exposure     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP229414     160653A_con_1_S6_L001_R1_001.fastq.gz 160653A_con_1_S6_L001_R2_001.fastq.gz 160653A_con_1_S6_L002_R1_001.fastq.gz 160653A_con_1_S6_L002_R2_001.fastq.gz fastq fastq fastq fastq 4387536203.0 17538394.0 160653A con 1 S6 L001 R1 001.fastq.gz 0:125.06 1:125.11 A:1178097571;C:999772360;G:1005888816;T:1180262110;N:23515346 125 125     1178097571 999772360 1005888816 1180262110 23515346 SRX7121460 SRS5631392 SRA993820 Chinese academy of fishery sciences|fishery Resource and Environmental Research Center Chinese academy of fishery sciences 2 0.92006 0.92409 0.13074 0.13101 0.66263 0.66505 0.4728 0.47345 126 126 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2019-11-11 Larval Larval Embryo Imprecise All anatomical structures
58872 58872 SRR11510448 SRX8082500 SRS6450585 SRP255712 PRJNA623798 Single cell lineage tracing on endogenous scarring sites scLOESS PRJNA623798 Other Lineage recording of zebrafish embryogenesis reveals early cell fate commitment     The developmental history of a whole zebrafish organism were recording by LOESS Lineage tracing Of Endogenous Scarring Sites technique. And both cell lineage histories and cell molecular profile were reconstructed by single cell RNA Seq profiling with the help of single cell sequencing methods and self developed analysis strategies. Single Cell RNA Seq of a whole organism of zebrafish larva SC   strain:AB line|age:7dpf|dev stage:larvae|sex:not applicable|tissue:Whole organism|collection date:2018 07 26|BioSampleModel:Model organism or animal                 Single Cell RNA Seq of a whole organism of zebrafish larva SC L3 SC L3 Zebrafish embryo at one cell stage were micro injected with gRNA pool and Cas9 mRNA mixture and growth at standard condiction ttwo xxxdpf. Then a single larva were lysis into single cell suspension and the RNA profile were obtained by 10x Genomics Chromium Single Cell three prime Reagent Kits v2 Chemistry.     RNA-Seq TRANSCRIPTOMIC SINGLE CELL RT-PCR PAIRED ILLUMINA HiSeq X Ten   SRP255712     SC-I1_S1_L001_R1_001.fastq.gz SC-I1_S1_L001_R2_001.fastq.gz SC-I1_S1_L002_R1_001.fastq.gz SC-I1_S1_L002_R2_001.fastq.gz SC-I1_S1_L003_R1_001.fastq.gz SC-I1_S1_L003_R2_001.fastq.gz SC-I2_S1_L001_R1_001.fastq.gz SC-I2_S1_L001_R2_001.fastq.gz SC-I2_S1_L002_R1_001.fastq.gz SC-I2_S1_L002_R2_001.fastq.gz SC-I2_S1_L003_R1_001.fastq.gz SC-I2_S1_L003_R2_001.fastq.gz SC-I3_S1_L001_R1_001.fastq.gz SC-I3_S1_L001_R2_001.fastq.gz SC-I3_S1_L002_R1_001.fastq.gz SC-I3_S1_L002_R2_001.fastq.gz SC-I3_S1_L003_R1_001.fastq.gz SC-I3_S1_L003_R2_001.fastq.gz SC-I4_S1_L001_R1_001.fastq.gz SC-I4_S1_L001_R2_001.fastq.gz SC-I4_S1_L002_R1_001.fastq.gz SC-I4_S1_L002_R2_001.fastq.gz SC-I4_S1_L003_R1_001.fastq.gz SC-I4_S1_L003_R2_001.fastq.gz fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq 86925323584.0 493893884.0 SC I1 S1 L001 R1 001.fastq.gz 0:26 1:150 A:24075189135;C:19816237204;G:21200277502;T:21828035227;N:5584516 26 150     24075189135 19816237204 21200277502 21828035227 5584516 SRX8082500 SRS6450585 SRA1063827 Sun Yat- sen University|Life Sicence School Sun Yat- sen University 2 0.00528 0.77254 0.00115 0.06529 0.98729 0.8158 0.41854 0.50141 26 150 T B sc-like readlen illumina hiseq_era unknown other unknown sc single_cell_droplet 10x   China 2020-04-11 Larval Larval Whole Organism All anatomical structures
58991 58991 SRR11577236 SRX8145127 SRS6507863 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 iso 5 20170222A 5dpf iso   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 22|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:5|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A016 A016 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170222A_5dpf_iso_S10_R1_001.fastq.gz fastq 1145417285.0 8785034.0 20170222A 5dpf iso S10 R1 001.fastq.gz 0:130.38 1:0 A:322759854;C:242145737;G:242143184;T:336959770;N:1408740 130 0     322759854 242145737 242143184 336959770 1408740 SRX8145127 SRS6507863 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93521   0.17614   0.66411   0.49656   109   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
58992 58992 SRR11577237 SRX8145126 SRS6507862 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 social 5 20170222A 5dpf soc   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 22|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:5|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A015 A015 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170222A_5dpf_soc_S9_R1_001.fastq.gz fastq 1951935848.0 15606984.0 20170222A 5dpf soc S9 R1 001.fastq.gz 0:125.07 1:0 A:546425279;C:412941736;G:422316572;T:568807662;N:1444599 125 0     546425279 412941736 422316572 568807662 1444599 SRX8145126 SRS6507862 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93665   0.17342   0.65971   0.50276   135   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
58993 58993 SRR11577238 SRX8145125 SRS6507861 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 iso 4 20170210B 5dpf iso   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 10|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:4|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A014 A014 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170210B_5dpf_iso_S8_R1_001.fastq.gz fastq 1438281543.0 10175957.0 20170210B 5dpf iso S8 R1 001.fastq.gz 0:141.34 1:0 A:405893769;C:302927323;G:299208098;T:428334452;N:1917901 141 0     405893769 302927323 299208098 428334452 1917901 SRX8145125 SRS6507861 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.9398   0.14632   0.66225   0.50935   150   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
58994 58994 SRR11577239 SRX8145124 SRS6507860 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 social 4 20170210B 5dpf soc   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 10|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:4|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A013 A013 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170210B_5dpf_soc_S7_R1_001.fastq.gz fastq 2086284546.0 17392851.0 20170210B 5dpf soc S7 R1 001.fastq.gz 0:119.95 1:0 A:564323359;C:455998854;G:458642653;T:599704356;N:7615324 119 0     564323359 455998854 458642653 599704356 7615324 SRX8145124 SRS6507860 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94679   0.14294   0.66724   0.49719   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
58995 58995 SRR11577240 SRX8145123 SRS6507859 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 iso 3 20170210A 5dpf iso   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 10|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A012 A012 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170210A_5dpf_iso_S6_R1_001.fastq.gz fastq 1518854121.0 12280862.0 20170210A 5dpf iso S6 R1 001.fastq.gz 0:123.68 1:0 A:416560027;C:326775060;G:324773078;T:444339405;N:6406551 123 0     416560027 326775060 324773078 444339405 6406551 SRX8145123 SRS6507859 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94696   0.13785   0.65969   0.50295   93   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59001 59001 SRR11577246 SRX8145117 SRS6507853 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 social 3 20170210A 5dpf soc   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 10|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A007 A007 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170210A_5dpf_soc_S5_R1_001.fastq.gz fastq 1726237934.0 14278894.0 20170210A 5dpf soc S5 R1 001.fastq.gz 0:120.89 1:0 A:463605810;C:370696125;G:372572642;T:495475185;N:23888172 120 0     463605810 370696125 372572642 495475185 23888172 SRX8145117 SRS6507853 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94821   0.14237   0.66689   0.48963   136   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59008 59008 SRR11577253 SRX8145110 SRS6507846 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 iso 6 20171109 8dpf iso B   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 09|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:6|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D508 D710 D508 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171109_8dpf_iso_B_S22_R1_001.fastq.gz fastq 1700207946.0 12434052.0 20171109 8dpf iso B S22 R1 001.fastq.gz 0:136.74 1:0 A:521541858;C:336119080;G:332771490;T:509018316;N:757202 136 0     521541858 336119080 332771490 509018316 757202 SRX8145110 SRS6507846 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93058   0.19578   0.68868   0.50184   139   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59009 59009 SRR11577254 SRX8145109 SRS6507845 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 social 6 20171109 8dpf soc B   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 09|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:6|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D507 D710 D507 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171109_8dpf_soc_B_S21_R1_001.fastq.gz fastq 2564439613.0 18763192.0 20171109 8dpf soc B S21 R1 001.fastq.gz 0:136.67 1:0 A:790757790;C:503826332;G:501530520;T:767769522;N:555449 136 0     790757790 503826332 501530520 767769522 555449 SRX8145109 SRS6507845 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92839   0.1986   0.68885   0.50483   131   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59010 59010 SRR11577255 SRX8145108 SRS6507844 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 iso 5 20171026 8dpf iso   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 10 26|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:5|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D506 D710 D506 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171026_8dpf_iso_S20_R1_001.fastq.gz fastq 2826413292.0 20452973.0 20171026 8dpf iso S20 R1 001.fastq.gz 0:138.19 1:0 A:865014614;C:559489084;G:552925517;T:847716596;N:1267481 138 0     865014614 559489084 552925517 847716596 1267481 SRX8145108 SRS6507844 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92608   0.2105   0.67903   0.49051   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59011 59011 SRR11577256 SRX8145107 SRS6507843 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 social 5 20171026 8dpf soc   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 10 26|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:5|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D505 D710 D505 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171026_8dpf_soc_S19_R1_001.fastq.gz fastq 2392544953.0 17491839.0 20171026 8dpf soc S19 R1 001.fastq.gz 0:136.78 1:0 A:742679673;C:465343974;G:462989237;T:721074201;N:457868 136 0     742679673 465343974 462989237 721074201 457868 SRX8145107 SRS6507843 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92316   0.21835   0.68655   0.48878   98   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59012 59012 SRR11577257 SRX8145106 SRS6507842 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 iso 2 20170209 5dpf iso   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 09|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A006 A006 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170209_5dpf_iso_S4_R1_001.fastq.gz fastq 1425974682.0 10933160.0 20170209 5dpf iso S4 R1 001.fastq.gz 0:130.43 1:0 A:384119497;C:314204651;G:311289822;T:412270680;N:4090032 130 0     384119497 314204651 311289822 412270680 4090032 SRX8145106 SRS6507842 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94694   0.14009   0.66271   0.50186   35   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59013 59013 SRR11577258 SRX8145105 SRS6507841 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 iso 4 20171019 8dpf iso   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 10 19|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:4|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D504 D710 D504 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171019_8dpf_iso_S18_R1_001.fastq.gz fastq 1983037322.0 14462095.0 20171019 8dpf iso S18 R1 001.fastq.gz 0:137.12 1:0 A:615819850;C:385988693;G:385056417;T:595787232;N:385130 137 0     615819850 385988693 385056417 595787232 385130 SRX8145105 SRS6507841 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92714   0.20602   0.68387   0.49262   150   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59014 59014 SRR11577259 SRX8145104 SRS6507840 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 social 4 20171019 8dpf soc   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 10 19|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:4|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D503 D710 D503 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171019_8dpf_soc_S17_R1_001.fastq.gz fastq 2128354590.0 15330724.0 20171019 8dpf soc S17 R1 001.fastq.gz 0:138.83 1:0 A:664838663;C:412783437;G:406007808;T:644520130;N:204552 138 0     664838663 412783437 406007808 644520130 204552 SRX8145104 SRS6507840 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92294   0.21336   0.68907   0.48677   112   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59015 59015 SRR11577260 SRX8145103 SRS6507839 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 iso 3 20170921 8dpf iso   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 21|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D502 D710 D502 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170921_8dpf_iso_S16_R1_001.fastq.gz fastq 1715158999.0 12523396.0 20170921 8dpf iso S16 R1 001.fastq.gz 0:136.96 1:0 A:517292645;C:345214588;G:340081628;T:512406926;N:163212 136 0     517292645 345214588 340081628 512406926 163212 SRX8145103 SRS6507839 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93065   0.1956   0.67543   0.48715   112   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59016 59016 SRR11577261 SRX8145102 SRS6507838 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 social 3 20170921 8dpf soc   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 09 21|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:3|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D710 D501 D710 D501 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170921_8dpf_soc_S15_R1_001.fastq.gz fastq 1903374830.0 13985406.0 20170921 8dpf soc S15 R1 001.fastq.gz 0:136.10 1:0 A:576312482;C:382917713;G:376058448;T:567672351;N:413836 136 0     576312482 382917713 376058448 567672351 413836 SRX8145102 SRS6507838 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.928   0.20225   0.68079   0.47235   139   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59023 59023 SRR11577268 SRX8145095 SRS6507831 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 social 2 20170209 5dpf soc   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 09|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A005 A005 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170209_5dpf_soc_S3_R1_001.fastq.gz fastq 932021340.0 8105951.0 20170209 5dpf soc S3 R1 001.fastq.gz 0:114.98 1:0 A:242483339;C:210201362;G:210814912;T:264386634;N:4135093 114 0     242483339 210201362 210814912 264386634 4135093 SRX8145095 SRS6507831 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.95059   0.13154   0.66099   0.48071   86   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59028 59028 SRR11577273 SRX8145090 SRS6507826 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 social 2 20171109 8dpf soc   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 09|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D708 D504 D708 D504 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171109__8dpf_soc_S4_R1_001.fastq.gz fastq 3315005132.0 25084324.0 20171109 8dpf soc S4 R1 001.fastq.gz 0:132.15 1:0 A:943965767;C:716020466;G:709793117;T:943523271;N:1702511 132 0     943965767 716020466 709793117 943523271 1702511 SRX8145090 SRS6507826 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94089   0.15844   0.68314   0.48662   150   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59029 59029 SRR11577274 SRX8145089 SRS6507825 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 iso 2 20171109 8dpf iso   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 09|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:2|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D708 D503 D708 D503 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171109__8dpf_iso_S3_R1_001.fastq.gz fastq 2050353509.0 15447845.0 20171109 8dpf iso S3 R1 001.fastq.gz 0:132.73 1:0 A:587865535;C:439314529;G:435742480;T:586757262;N:673703 132 0     587865535 439314529 435742480 586757262 673703 SRX8145089 SRS6507825 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93978   0.1602   0.67381   0.48469   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59030 59030 SRR11577275 SRX8145088 SRS6507824 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 social 1 20171102 8dpf soc   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 02|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D708 D502 D708 D502 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171102__8dpf_soc_S2_R1_001.fastq.gz fastq 1343770858.0 9948770.0 20171102 8dpf soc S2 R1 001.fastq.gz 0:135.07 1:0 A:393209270;C:281371562;G:280065221;T:388373414;N:751391 135 0     393209270 281371562 280065221 388373414 751391 SRX8145088 SRS6507824 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93753   0.16528   0.67478   0.48859   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59031 59031 SRR11577276 SRX8145087 SRS6507823 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       8 iso 1 20171102 8dpf iso   breed:Konstanz Wildtype|age:8 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 11 02|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain D708 D501 D708 D501 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20171102__8dpf_iso_S1_R1_001.fastq.gz fastq 2222891523.0 16512518.0 20171102 8dpf iso S1 R1 001.fastq.gz 0:134.62 1:0 A:612900253;C:492583648;G:489352034;T:626301202;N:1754386 134 0     612900253 492583648 489352034 626301202 1754386 SRX8145087 SRS6507823 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94375   0.14492   0.67117   0.4862   150   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59032 59032 SRR11577277 SRX8145086 SRS6507822 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 iso 6 20170222B 5dpf iso   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 22|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:6|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A019 A019 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170222B_5dpf_iso_S12_R1_001.fastq.gz fastq 1384115190.0 10880190.0 20170222B 5dpf iso S12 R1 001.fastq.gz 0:127.21 1:0 A:374024483;C:300637678;G:306091186;T:396608297;N:6753546 127 0     374024483 300637678 306091186 396608297 6753546 SRX8145086 SRS6507822 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.93966   0.14845   0.66145   0.49277   135   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59033 59033 SRR11577278 SRX8145085 SRS6507821 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 social 6 20170222B 5dpf soc   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 22|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:6|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A018 A018 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170222B_5dpf_soc_S11_R1_001.fastq.gz fastq 1509062868.0 11709685.0 20170222B 5dpf soc S11 R1 001.fastq.gz 0:128.87 1:0 A:424881841;C:317025415;G:321339469;T:440828991;N:4987152 128 0     424881841 317025415 321339469 440828991 4987152 SRX8145085 SRS6507821 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.92918   0.18084   0.67067   0.48693   113   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59034 59034 SRR11577279 SRX8145084 SRS6507820 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 iso 1 20170201 5pdf iso   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 01|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:isolated|replicate:1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A004 A004 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170201_5pdf_iso_S2_R1_001.fastq.gz fastq 2182551927.0 16660472.0 20170201 5pdf iso S2 R1 001.fastq.gz 0:131.00 1:0 A:585229301;C:487317339;G:480857079;T:626932180;N:2216028 131 0     585229301 487317339 480857079 626932180 2216028 SRX8145084 SRS6507820 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94677   0.13688   0.6633   0.47121   145   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
59035 59035 SRR11577280 SRX8145083 SRS6507819 SRP257630 PRJNA627056 Impact of social isolation on brain transcriptome in zebrafish PRJNA627056 Other The goal of the study was to identify genes or genetic modules that are associated with the presence/absence of conspecifics.       5 social 1 20170201 5dpf soc   breed:Konstanz Wildtype|age:5 dpf|dev stage:larva|sex:not applicable|tissue:brain|biomaterial provider:Erin Schuman|collected by:Lukas Anneser|collection date:2017 02 01|sample type:whole brain|store cond:storage in trizol immediate extraction|treatment:social|replicate:1|BioSampleModel:Model organism or animal                 RNA Seq of danio rerio: larval and juvenile brain A002 A002 RNA extraction from whole brain lysates polyA enrichment reverse transcription and amplification     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA NextSeq 500   SRP257630     20170201_5dpf_soc_S1_R1_001.fastq.gz fastq 1713105557.0 13585484.0 20170201 5dpf soc S1 R1 001.fastq.gz 0:126.10 1:0 A:446628660;C:370803315;G:376374066;T:481602204;N:37697312 126 0     446628660 370803315 376374066 481602204 37697312 SRX8145083 SRS6507819 SRA1067479 Max Planck Institute for Brain Research|Synaptic Plasticity Max Planck Institute for Brain Research 1 0.94527   0.13591   0.66302   0.48385   151   B   usable mapping rate illumina nextseq unknown poly_a unknown bulk unknown unknown   Germany 2020-04-21 Larval Larval Brain Nervous System
66745 66745 SRR16530663 SRX12733276 SRS10681588 SRP342649 PRJNA773625 loft ventricle RNAseq PRJNA773625 Other Cardiac looping and trabeculation are key processes during cardiac chamber maturation and alteration of these processes frequently causes congenital heart defects. Here we report the isolation cloning and characterization of the proprotein convertase furina from the cardiovascular mutant loft in zebrafish and thus establish its critical role in heart looping and trabecular development. Although heart defects are previously reported in zebrafish and mouse furin mutants it remains unclear what are the targets of Furin in the heart. This work presents a new layer of post translational modulation of Notch1b proteins by Furina during zebrafish cardiac looping and trabeculation and mutations in the Furina Notch1b axis may shed light on the genetic basis of congenital heart diseases in humans.       RNAseq of zebrafish heart loft mutant RNAseq rep2   strain:Tu|dev stage:3 dpf determined|tissue:ventricle|genotype:loft mutant|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNAseq of zebrafish heart loft mutant RNAseq rep2 loft mutant RNAseq rep2 The cDNA libraries were constructed by MALBAC method KT110700424 Yikon Genomics     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP342649   assembly:danRer7 loft_mutant_RNAseq_rep2.1.bam loft_mutant_RNAseq_rep2.2.bam bam bam 4184284762.0 20714281.0 loft mutant RNAseq rep2.1.bam 0:101 1:101 A:1235933017;C:598023900;G:852833672;T:1497442499;N:51674 101 101     1235933017 598023900 852833672 1497442499 51674 SRX12733276 SRS10681588 SRA1315131 Peking University|Institute of Molecular Medicine Peking University 2 0.4825 0.50527 0.2448 0.25451 0.87288 0.87888 0.46562 0.45703 101 101 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2021-10-22 Larval Larval Heart Cardiovascular System
66746 66746 SRR16530664 SRX12733275 SRS10681587 SRP342649 PRJNA773625 loft ventricle RNAseq PRJNA773625 Other Cardiac looping and trabeculation are key processes during cardiac chamber maturation and alteration of these processes frequently causes congenital heart defects. Here we report the isolation cloning and characterization of the proprotein convertase furina from the cardiovascular mutant loft in zebrafish and thus establish its critical role in heart looping and trabecular development. Although heart defects are previously reported in zebrafish and mouse furin mutants it remains unclear what are the targets of Furin in the heart. This work presents a new layer of post translational modulation of Notch1b proteins by Furina during zebrafish cardiac looping and trabeculation and mutations in the Furina Notch1b axis may shed light on the genetic basis of congenital heart diseases in humans.       RNAseq of zebrafish heart loft mutant RNAseq rep1   strain:Tu|dev stage:3 dpf determined|tissue:ventricle|genotype:loft mutant|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNAseq of zebrafish heart loft mutant RNAseq rep1 loft mutant RNAseq rep1 The cDNA libraries were constructed by MALBAC method KT110700424 Yikon Genomics     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP342649   assembly:danRer7 loft_mutant_RNAseq_rep1.1.bam loft_mutant_RNAseq_rep1.2.bam bam bam 4349194532.0 21530666.0 loft mutant RNAseq rep1.1.bam 0:101 1:101 A:1285307324;C:607005074;G:876055199;T:1580773245;N:53690 101 101     1285307324 607005074 876055199 1580773245 53690 SRX12733275 SRS10681587 SRA1315131 Peking University|Institute of Molecular Medicine Peking University 2 0.50395 0.50527 0.2163 0.21684 0.87444 0.88371 0.47374 0.46918 101 101 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2021-10-22 Larval Larval Heart Cardiovascular System
66747 66747 SRR16530665 SRX12733274 SRS10681586 SRP342649 PRJNA773625 loft ventricle RNAseq PRJNA773625 Other Cardiac looping and trabeculation are key processes during cardiac chamber maturation and alteration of these processes frequently causes congenital heart defects. Here we report the isolation cloning and characterization of the proprotein convertase furina from the cardiovascular mutant loft in zebrafish and thus establish its critical role in heart looping and trabecular development. Although heart defects are previously reported in zebrafish and mouse furin mutants it remains unclear what are the targets of Furin in the heart. This work presents a new layer of post translational modulation of Notch1b proteins by Furina during zebrafish cardiac looping and trabeculation and mutations in the Furina Notch1b axis may shed light on the genetic basis of congenital heart diseases in humans.       RNAseq of zebrafish heart loft sibling RNAseq rep2   strain:Tu|dev stage:3 dpf determined|tissue:ventricle|genotype:loft sibling|replicate:biological replicate 2|BioSampleModel:Model organism or animal                 RNAseq of zebrafish heart loft sibling RNAseq rep2 loft sibling RNAseq rep2 The cDNA libraries were constructed by MALBAC method KT110700424 Yikon Genomics     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP342649   assembly:danRer7 loft_sibling_RNAseq_rep2.1.bam loft_sibling_RNAseq_rep2.2.bam bam bam 3901869168.0 19316184.0 loft sibling RNAseq rep2.1.bam 0:101 1:101 A:1145110581;C:555289006;G:798238595;T:1403183360;N:47626 101 101     1145110581 555289006 798238595 1403183360 47626 SRX12733274 SRS10681586 SRA1315131 Peking University|Institute of Molecular Medicine Peking University 2 0.47753 0.48927 0.20347 0.20928 0.86994 0.87726 0.46911 0.43318 101 101 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2021-10-22 Larval Larval Heart Cardiovascular System
66748 66748 SRR16530666 SRX12733273 SRS10681585 SRP342649 PRJNA773625 loft ventricle RNAseq PRJNA773625 Other Cardiac looping and trabeculation are key processes during cardiac chamber maturation and alteration of these processes frequently causes congenital heart defects. Here we report the isolation cloning and characterization of the proprotein convertase furina from the cardiovascular mutant loft in zebrafish and thus establish its critical role in heart looping and trabecular development. Although heart defects are previously reported in zebrafish and mouse furin mutants it remains unclear what are the targets of Furin in the heart. This work presents a new layer of post translational modulation of Notch1b proteins by Furina during zebrafish cardiac looping and trabeculation and mutations in the Furina Notch1b axis may shed light on the genetic basis of congenital heart diseases in humans.       RNAseq of zebrafish heart loft sibling RNAseq rep1   strain:Tu|dev stage:3 dpf determined|tissue:ventricle|genotype:loft sibling|replicate:biological replicate 1|BioSampleModel:Model organism or animal                 RNAseq of zebrafish heart loft sibling RNAseq rep1 loft sibling RNAseq rep1 The cDNA libraries were constructed by MALBAC method KT110700424 Yikon Genomics     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP342649   assembly:danRer7 loft_sibling_RNAseq_rep1.1.bam loft_sibling_RNAseq_rep1.2.bam bam bam 3973568260.0 19671130.0 loft sibling RNAseq rep1.1.bam 0:101 1:101 A:1171529555;C:572236920;G:816914171;T:1412839393;N:48221 101 101     1171529555 572236920 816914171 1412839393 48221 SRX12733273 SRS10681585 SRA1315131 Peking University|Institute of Molecular Medicine Peking University 2 0.47895 0.47714 0.25104 0.24998 0.86841 0.87568 0.46945 0.47273 101 101 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2021-10-22 Larval Larval Heart Cardiovascular System
69631 69631 SRR19025949 SRX15097731 SRS12843022 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       trmt5 knock out zebrafish trmt5 / 1   isolate:total RNAs isolated from trmt5 knock out zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish 66ff83cdf42005466331679c80f92d12 66ff83cdf42005466331679c80f92d12 trmt5 knock out zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     hom_1_Clean_Data2.fq.gz hom_1_Clean_Data1.fq.gz fastq fastq 6169235123.0 21958377.0 hom 1 Clean Data1.fq.gz 0:140.50 1:140.46 A:1560853223;C:1511690807;G:1520013294;T:1576470786;N:207013 140 140     1560853223 1511690807 1520013294 1576470786 207013 SRX15097731 SRS12843022 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96859 0.96977 0.0392 0.03772 0.70658 0.70751 0.49243 0.49647 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69632 69632 SRR19025950 SRX15097730 SRS12843021 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       wild type zebrafish trmt5+/+ 4   isolate:total RNAs isolated from WT zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish d919fe9c401838b06040e4ee1638981e d919fe9c401838b06040e4ee1638981e wild type zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     wt_4_Clean_Data1.fq.gz wt_4_Clean_Data2.fq.gz fastq fastq 6033250663.0 21483270.0 wt 4 Clean Data1.fq.gz 0:140.44 1:140.40 A:1538261833;C:1466011430;G:1475787704;T:1552985419;N:204277 140 140     1538261833 1466011430 1475787704 1552985419 204277 SRX15097730 SRS12843021 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96586 0.96804 0.04584 0.04451 0.68698 0.68688 0.46575 0.44961 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69633 69633 SRR19025951 SRX15097729 SRS12843020 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       wild type zebrafish trmt5+/+ 3   isolate:total RNAs isolated from WT zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish d0459b1dac26131278f334c9290f1d2b d0459b1dac26131278f334c9290f1d2b wild type zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     wt_3_Clean_Data2.fq.gz wt_3_Clean_Data1.fq.gz fastq fastq 5891772865.0 20970124.0 wt 3 Clean Data1.fq.gz 0:140.50 1:140.46 A:1502638659;C:1431652346;G:1439973482;T:1517318614;N:189764 140 140     1502638659 1431652346 1439973482 1517318614 189764 SRX15097729 SRS12843020 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96668 0.96871 0.04432 0.04253 0.6887 0.68842 0.46997 0.45735 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69634 69634 SRR19025952 SRX15097728 SRS12843019 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       wild type zebrafish trmt5+/+ 2   isolate:total RNAs isolated from WT zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish 9dbee5750238db2822304d9f2e0edea9 9dbee5750238db2822304d9f2e0edea9 wild type zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     wt_2_Clean_Data1.fq.gz wt_2_Clean_Data2.fq.gz fastq fastq 5766006501.0 20521262.0 wt 2 Clean Data1.fq.gz 0:140.51 1:140.47 A:1470465676;C:1400491025;G:1410148993;T:1484706149;N:194658 140 140     1470465676 1400491025 1410148993 1484706149 194658 SRX15097728 SRS12843019 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96644 0.9675 0.04557 0.04323 0.68832 0.68842 0.4676 0.4602 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69635 69635 SRR19025953 SRX15097727 SRS12843018 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       trmt5 knock out zebrafish trmt5 / 4   isolate:total RNAs isolated from trmt5 knock out zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate4|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish 7a076bcf71269def10954f4107bf1124 7a076bcf71269def10954f4107bf1124 trmt5 knock out zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     hom_4_Clean_Data1.fq.gz hom_4_Clean_Data2.fq.gz fastq fastq 6241361550.0 22218760.0 hom 4 Clean Data1.fq.gz 0:140.47 1:140.43 A:1577557316;C:1530905024;G:1539141855;T:1593551612;N:205743 140 140     1577557316 1530905024 1539141855 1593551612 205743 SRX15097727 SRS12843018 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.97042 0.97147 0.03889 0.03706 0.71035 0.71062 0.48557 0.50047 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69636 69636 SRR19025954 SRX15097726 SRS12843017 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       trmt5 knock out zebrafish trmt5 / 3   isolate:total RNAs isolated from trmt5 knock out zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate3|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish 5689e7391d2921855b4759bcdc123378 5689e7391d2921855b4759bcdc123378 trmt5 knock out zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     hom_3_Clean_Data1.fq.gz hom_3_Clean_Data2.fq.gz fastq fastq 6051656240.0 21549593.0 hom 3 Clean Data1.fq.gz 0:140.43 1:140.39 A:1531682742;C:1482500631;G:1490088770;T:1547184370;N:199727 140 140     1531682742 1482500631 1490088770 1547184370 199727 SRX15097726 SRS12843017 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96902 0.97138 0.03966 0.03849 0.71208 0.71244 0.49461 0.4851 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69637 69637 SRR19025955 SRX15097725 SRS12843016 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       trmt5 knock out zebrafish trmt5 / 2   isolate:total RNAs isolated from trmt5 knock out zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate2|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish 8b1e5ab49c8be853af71803609cb227c 8b1e5ab49c8be853af71803609cb227c trmt5 knock out zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     hom_2_Clean_Data1.fq.gz hom_2_Clean_Data2.fq.gz fastq fastq 6212537192.0 22136506.0 hom 2 Clean Data1.fq.gz 0:140.34 1:140.31 A:1573896925;C:1526845773;G:1529170873;T:1582416723;N:206898 140 140     1573896925 1526845773 1529170873 1582416723 206898 SRX15097725 SRS12843016 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96821 0.96875 0.03881 0.03757 0.71259 0.71285 0.48811 0.48638 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
69638 69638 SRR19025956 SRX15097724 SRS12843015 SRP373069 PRJNA833575 RNA sequencing analysis of wildtype and trmt5 knock out zebrafish PRJNA833575 Other Having clarified the alternated histological properties in trmt5 null zebrafish we were curious about the differences at the molecular level induced by trmt5 depletion. Whole body total RNAs samples were prepared from trmt5 / mutants and wide type siblings larvae at 16 dpf and RNA sequencing analysis was performed.       wild type zebrafish trmt5+/+ 1   isolate:total RNAs isolated from WT zebrafish|age:16 dpf|dev stage:larval stage|sex:N1|tissue:whole body|replicate:replicate1|BioSampleModel:Model organism or animal                 RNA Seq of zebrafish acd6771912bd9a4423df64fa4898e484 acd6771912bd9a4423df64fa4898e484 wild type zebrafish     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina NovaSeq 6000   SRP373069     wt_1_Clean_Data1.fq.gz wt_1_Clean_Data2.fq.gz fastq fastq 6143077598.0 21878233.0 wt 1 Clean Data1.fq.gz 0:140.41 1:140.38 A:1578226894;C:1486538531;G:1490138396;T:1587966031;N:207746 140 140     1578226894 1486538531 1490138396 1587966031 207746 SRX15097724 SRS12843015 SRA1412777 Zhejiang University|Division of Medical Genetics and Genomics Zhejiang University 2 0.96278 0.96429 0.05204 0.05046 0.67817 0.67978 0.45055 0.43833 141 141 B B biological fallback assumption illumina novaseq_era unknown other unknown bulk unknown unknown   China 2022-05-02 Larval Larval Trunk Surface Structure
71545 71545 SRR21784852 SRX17779292 SRS15305447 SRP400746 PRJNA883515 Danio rerio Transcriptome or Gene expression PRJNA883515 Other Carassius auratus complex formula CACF is a combination prescription of traditional Chinese medicine composed of extracts from C. auratus Rhizoma dioscoreae Lycium chinense and Rehmannia glutinosa Libosch. Previously CACF has been proven the anti diabetes effect on HFD treatment mice model. In this study we used zebrafish model to observe whether CACF have anti cancer effect or not.       Model organism or animal sample from Danio rerio Normal diet 1 1 CD36 normal diet 1 1   ecotype:Taiwan ROC|age:15 dpf|dev stage:larvae|sex:not determined|tissue:whole fish|BioSampleModel:Model organism or animal                 RNA seq of CD36 normal diet fish 1 1 C15D 12 1 1 C15D 12 1 1 the zebrafish larvae fed with normal diet from 5dpf to 15 dpf and fast for two days then sacrificed to extract the total RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiScanSQ   SRP400746     C15D_12_1_1_paired C15D_12_1_2_paired fastq fastq 5223003761.0 17590299.0 C15D 12 1 1 paired 0:148.55 1:148.38 A:1369931254;C:1227975299;G:1223263204;T:1401778621;N:55383 148 148     1369931254 1227975299 1223263204 1401778621 55383 SRX17779292 SRS15305447 SRA1511182 National Health Research Institutes|Institute of Molecular and Genomic Medicine National Health Research Institutes 2 0.94554 0.94659 0.11224 0.11161 0.71898 0.71849 0.56127 0.55388 151 151 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   Taiwan 2022-10-03 Larval Larval Whole Organism All anatomical structures
71546 71546 SRR21784853 SRX17779291 SRS15305446 SRP400746 PRJNA883515 Danio rerio Transcriptome or Gene expression PRJNA883515 Other Carassius auratus complex formula CACF is a combination prescription of traditional Chinese medicine composed of extracts from C. auratus Rhizoma dioscoreae Lycium chinense and Rehmannia glutinosa Libosch. Previously CACF has been proven the anti diabetes effect on HFD treatment mice model. In this study we used zebrafish model to observe whether CACF have anti cancer effect or not.       Model organism or animal sample from Danio rerio CACF 2 1 CD36 CACF 2 1   ecotype:Taiwan ROC|age:15 dpf|dev stage:larvae|sex:not determined|tissue:whole fish|BioSampleModel:Model organism or animal                 RNA seq of CD36 with CACF treatment fish 1 1 T15D 24 C 2 1 T15D 24 C 2 1 the zebrafish larvae fed with hight fat diet and treat with CACF everyday from 5dpf to 15 dpf and fast for two days then sacrificed to extract the total RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiScanSQ   SRP400746     T15D_24_C_2_1_paired T15D_24_C_2_2_paired fastq fastq 3981831028.0 13417594.0 T15D 24 C 2 1 paired 0:148.59 1:148.17 A:1093541197;C:886197071;G:886629442;T:1115421463;N:41855 148 148     1093541197 886197071 886629442 1115421463 41855 SRX17779291 SRS15305446 SRA1511182 National Health Research Institutes|Institute of Molecular and Genomic Medicine National Health Research Institutes 2 0.94081 0.94152 0.10901 0.10793 0.70964 0.70855 0.602 0.60183 151 151 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   Taiwan 2022-10-03 Larval Larval Whole Organism All anatomical structures
71547 71547 SRR21784854 SRX17779290 SRS15305445 SRP400746 PRJNA883515 Danio rerio Transcriptome or Gene expression PRJNA883515 Other Carassius auratus complex formula CACF is a combination prescription of traditional Chinese medicine composed of extracts from C. auratus Rhizoma dioscoreae Lycium chinense and Rehmannia glutinosa Libosch. Previously CACF has been proven the anti diabetes effect on HFD treatment mice model. In this study we used zebrafish model to observe whether CACF have anti cancer effect or not.       Model organism or animal sample from Danio rerio CACF 4 1 CD36 CACF 4 1   ecotype:Taiwan ROC|age:15 dpf|dev stage:larvae|sex:not determined|tissue:whole fish|BioSampleModel:Model organism or animal                 RNA seq of CD36 with CACF treatment fish 2 1 T15D 24 C 4 1 T15D 24 C 4 1 the zebrafish larvae fed with hight fat diet and treat with CACF everyday from 5dpf to 15 dpf and fast for two days then sacrificed to extract the total RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiScanSQ   SRP400746     T15D_24_C_4_1_paired T15D_24_C_4_2_paired fastq fastq 4676812747.0 15766218.0 T15D 24 C 4 1 paired 0:148.04 1:148.60 A:1264847140;C:1061075206;G:1060248997;T:1290593882;N:47522 148 148     1264847140 1061075206 1060248997 1290593882 47522 SRX17779290 SRS15305445 SRA1511182 National Health Research Institutes|Institute of Molecular and Genomic Medicine National Health Research Institutes 2 0.92949 0.93109 0.12219 0.12166 0.70343 0.70122 0.56431 0.56468 151 151 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   Taiwan 2022-10-03 Larval Larval Whole Organism All anatomical structures
71548 71548 SRR21784855 SRX17779289 SRS15305444 SRP400746 PRJNA883515 Danio rerio Transcriptome or Gene expression PRJNA883515 Other Carassius auratus complex formula CACF is a combination prescription of traditional Chinese medicine composed of extracts from C. auratus Rhizoma dioscoreae Lycium chinense and Rehmannia glutinosa Libosch. Previously CACF has been proven the anti diabetes effect on HFD treatment mice model. In this study we used zebrafish model to observe whether CACF have anti cancer effect or not.       Model organism or animal sample from Danio rerio Normal diet 2 1 CD36 normal diet 2 1   ecotype:Taiwan ROC|age:15 dpf|dev stage:larvae|sex:not determined|tissue:whole fish|BioSampleModel:Model organism or animal                 RNA seq of CD36 normal diet fish 2 1 C15D 12 2 1 C15D 12 2 1 the zebrafish larvae fed with normal diet from 5dpf to 15 dpf and fast for two days then sacrificed to extract the total RNA     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiScanSQ   SRP400746     C15D_12_2_1_paired C15D_12_2_2_paired fastq fastq 4709835299.0 15889935.0 C15D 12 2 1 paired 0:148.38 1:148.02 A:1276830997;C:1066019825;G:1064609195;T:1302325802;N:49480 148 148     1276830997 1066019825 1064609195 1302325802 49480 SRX17779289 SRS15305444 SRA1511182 National Health Research Institutes|Institute of Molecular and Genomic Medicine National Health Research Institutes 2 0.92935 0.9298 0.13602 0.1343 0.70747 0.70788 0.50602 0.50503 151 151 B B biological fallback assumption illumina early_illumina unknown other unknown bulk unknown unknown   Taiwan 2022-10-03 Larval Larval Whole Organism All anatomical structures
72097 72097 SRR22207161 SRX18185147 SRS15683480 SRP406513 PRJNA898663 zebrafish Raw sequence reads PRJNA898663 Other High throughput sequencing of LOXHD1B gene knockdown and control in zebrafish         L3   isolate:Loxhd1b 3|age:5 days|sex:not determined|tissue:RNA|BioSampleModel:Model organism or animal                 RNA seq of zebrafish RNA: loxhd1b morpholino 3 GCS6 GCS6 Next generation sequencing library preparations were constructed according to the manufacturers protocol.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP406513     L3_combined_R1.fastq.gz L3_combined_R2.fastq.gz fastq fastq 6143010000.0 20476700.0 L3 combined R1.fastq.gz 0:150 1:150 A:1595745772;C:1478410203;G:1489224712;T:1579586384;N:42929 150 150     1595745772 1478410203 1489224712 1579586384 42929 SRX18185147 SRS15683480 SRA1535247 Shandong Provincial Hospital|Department of Clinical Laboratory Shandong Provincial Hospital 2 0.95627 0.95623 0.04743 0.04704 0.70256 0.7068 0.47182 0.4714 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-11-06 Larval Larval Undetermined Undetermined
72098 72098 SRR22207162 SRX18185146 SRS15683479 SRP406513 PRJNA898663 zebrafish Raw sequence reads PRJNA898663 Other High throughput sequencing of LOXHD1B gene knockdown and control in zebrafish         L2   isolate:Loxhd1b 2|age:5 days|sex:not determined|tissue:RNA|BioSampleModel:Model organism or animal                 RNA seq of zebrafish RNA: loxhd1b morpholino 2 GCS5 GCS5 Next generation sequencing library preparations were constructed according to the manufacturers protocol.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP406513     L2_combined_R1.fastq.gz L2_combined_R2.fastq.gz fastq fastq 6424738200.0 21415794.0 L2 combined R1.fastq.gz 0:150 1:150 A:1671624607;C:1543603819;G:1552613091;T:1656850928;N:45755 150 150     1671624607 1543603819 1552613091 1656850928 45755 SRX18185146 SRS15683479 SRA1535247 Shandong Provincial Hospital|Department of Clinical Laboratory Shandong Provincial Hospital 2 0.95661 0.95668 0.04747 0.04742 0.68856 0.69179 0.47314 0.48109 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-11-06 Larval Larval Undetermined Undetermined
72099 72099 SRR22207163 SRX18185145 SRS15683478 SRP406513 PRJNA898663 zebrafish Raw sequence reads PRJNA898663 Other High throughput sequencing of LOXHD1B gene knockdown and control in zebrafish         L1   isolate:Loxhd1b 1|age:5 days|sex:not determined|tissue:RNA|BioSampleModel:Model organism or animal                 RNA seq of zebrafish RNA: loxhd1b morpholino 1 GCS4 GCS4 Next generation sequencing library preparations were constructed according to the manufacturers protocol.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP406513     L1_combined_R1.fastq.gz L1_combined_R2.fastq.gz fastq fastq 7191693900.0 23972313.0 L1 combined R1.fastq.gz 0:150 1:150 A:1864938414;C:1733274971;G:1741654024;T:1851774229;N:52262 150 150     1864938414 1733274971 1741654024 1851774229 52262 SRX18185145 SRS15683478 SRA1535247 Shandong Provincial Hospital|Department of Clinical Laboratory Shandong Provincial Hospital 2 0.95471 0.95533 0.05078 0.05161 0.67844 0.68191 0.47707 0.48159 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-11-06 Larval Larval Undetermined Undetermined
72100 72100 SRR22207164 SRX18185144 SRS15683477 SRP406513 PRJNA898663 zebrafish Raw sequence reads PRJNA898663 Other High throughput sequencing of LOXHD1B gene knockdown and control in zebrafish         C3   isolate:control 3|age:5 days|sex:not determined|tissue:RNA|BioSampleModel:Model organism or animal                 RNA seq of zebrafish RNA: control 3 GCS3 GCS3 Next generation sequencing library preparations were constructed according to the manufacturers protocol.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP406513     C3_combined_R1.fastq.gz C3_combined_R2.fastq.gz fastq fastq 6332394900.0 21107983.0 C3 combined R1.fastq.gz 0:150 1:150 A:1627554436;C:1541108160;G:1544576517;T:1619111254;N:44533 150 150     1627554436 1541108160 1544576517 1619111254 44533 SRX18185144 SRS15683477 SRA1535247 Shandong Provincial Hospital|Department of Clinical Laboratory Shandong Provincial Hospital 2 0.95993 0.95944 0.04103 0.04133 0.68296 0.68779 0.48812 0.47385 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-11-06 Larval Larval Undetermined Undetermined
72101 72101 SRR22207165 SRX18185143 SRS15683476 SRP406513 PRJNA898663 zebrafish Raw sequence reads PRJNA898663 Other High throughput sequencing of LOXHD1B gene knockdown and control in zebrafish         C2   isolate:control 2|age:5 days|sex:not determined|tissue:RNA|BioSampleModel:Model organism or animal                 RNA seq of zebrafish RNA: control 2 GCS2 GCS2 Next generation sequencing library preparations were constructed according to the manufacturers protocol.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP406513     C2_combined_R1.fastq.gz C2_combined_R2.fastq.gz fastq fastq 6442334100.0 21474447.0 C2 combined R1.fastq.gz 0:150 1:150 A:1656988931;C:1570298030;G:1573573169;T:1641411583;N:62387 150 150     1656988931 1570298030 1573573169 1641411583 62387 SRX18185143 SRS15683476 SRA1535247 Shandong Provincial Hospital|Department of Clinical Laboratory Shandong Provincial Hospital 2 0.95971 0.96117 0.03893 0.03968 0.70692 0.71169 0.47551 0.47899 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-11-06 Larval Larval Undetermined Undetermined
72102 72102 SRR22207166 SRX18185142 SRS15683475 SRP406513 PRJNA898663 zebrafish Raw sequence reads PRJNA898663 Other High throughput sequencing of LOXHD1B gene knockdown and control in zebrafish         C1   isolate:control 1|age:5 days|sex:not determined|tissue:RNA|BioSampleModel:Model organism or animal                 RNA seq of zebrafish RNA: control 1 GCS1 GCS1 Next generation sequencing library preparations were constructed according to the manufacturers protocol.     RNA-Seq TRANSCRIPTOMIC RT-PCR PAIRED ILLUMINA Illumina HiSeq 2500   SRP406513     C1_combined_R1.fastq.gz C1_combined_R2.fastq.gz fastq fastq 6508720200.0 21695734.0 C1 combined R1.fastq.gz 0:150 1:150 A:1679478806;C:1581181952;G:1586326453;T:1661672060;N:60929 150 150     1679478806 1581181952 1586326453 1661672060 60929 SRX18185142 SRS15683475 SRA1535247 Shandong Provincial Hospital|Department of Clinical Laboratory Shandong Provincial Hospital 2 0.9598 0.96029 0.04091 0.04106 0.70834 0.71171 0.4832 0.48953 150 150 B B biological fallback assumption illumina hiseq_era unknown other unknown bulk unknown unknown   China 2022-11-06 Larval Larval Undetermined Undetermined
77327 77327 SRR065197 SRX026483 SRS114570 SRP003472 PRJXX3472 RNA Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation ZF_U1C Transcriptome Analysis Precise five prime splice site recognition is essential for both constitutive and regulated pre mRNA splicing. The U1 snRNP specific protein U1C is involved in this first step of spliceosome assembly and important for stabilizing early splicing complexes. We used an embryonically lethal U1C knockout mutant zebrafish hi1371 to investigate the potential genomewide role of U1C for splicing regulation. Surprisingly genomewide RNA Seq analysis of mutant versus wildtype embryos revealed a large set of specific target genes that changed their alternative splicing patterns in the absence of U1C. In sum our findings provide evidence for a new role of a general snRNP protein U1C as a mediator of alternative splicing regulation.   pubmed:21468032 Total RNA from 3 dpf mutant zebrafish embryos was prepared by TRIzol reagent Invitrogen and RNeasy kit QIAGEN. Equal amounts of total RNA were subjected to reverse transcription using the qScript cDNA synthesis kit Quanta Biosciences. Control reactions were done in the absence of reverse transcriptase. Total RNA was processed by Illumina standard protocols to prepare the RNA Seq library. Total RNA from 3 dpf mutant zebrafish embryos MUT                     3 dpf mutant zebrafish embryos MUT mut 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP003472     MUT_1.txt.tar.gz MUT_2N.txt.tar.gz MUT_3.txt.tar.gz fastq fastq fastq 2418427464.0 31821414.0 MUT 0:76 A:604956506;C:600954722;G:608767958;T:600808464;N:2939814 76       604956506 600954722 608767958 600808464 2939814 SRX026483 SRS114570     Justus-Liebig University Giessen 1 0.91109   0.077   0.71445   0.44387   76   B   usable mapping rate illumina early_illumina unknown other unknown bulk unknown unknown   Germany 2011-03-31 Larval Larval Embryo Imprecise All anatomical structures
77328 77328 SRR065196 SRX026482 SRS114569 SRP003472 PRJXX3472 RNA Seq analysis in mutant zebrafish reveals role of U1C protein in alternative splicing regulation ZF_U1C Transcriptome Analysis Precise five prime splice site recognition is essential for both constitutive and regulated pre mRNA splicing. The U1 snRNP specific protein U1C is involved in this first step of spliceosome assembly and important for stabilizing early splicing complexes. We used an embryonically lethal U1C knockout mutant zebrafish hi1371 to investigate the potential genomewide role of U1C for splicing regulation. Surprisingly genomewide RNA Seq analysis of mutant versus wildtype embryos revealed a large set of specific target genes that changed their alternative splicing patterns in the absence of U1C. In sum our findings provide evidence for a new role of a general snRNP protein U1C as a mediator of alternative splicing regulation.   pubmed:21468032 Total RNA from 3 dpf wildtype zebrafish embryos was prepared by TRIzol reagent Invitrogen and RNeasy kit QIAGEN. Equal amounts of total RNA were subjected to reverse transcription using the qScript cDNA synthesis kit Quanta Biosciences. Control reactions were done in the absence of reverse transcriptase. Total RNA was processed by Illumina standard protocols to prepare the RNA Seq library. Total RNA from 3 dpf wildtype zebrafish embryos WT                     3 dpf wildtype embryos WT wt 1     RNA-Seq TRANSCRIPTOMIC RT-PCR SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP003472     WT_1.txt.tar WT_2.txt.tar.gz WT_3.txt.tar.gz WT_4.txt.tar.gz fastq fastq fastq fastq 2697785376.0 35497176.0 WT 0:76 A:676186765;C:669131645;G:670872323;T:676745206;N:4849437 76       676186765 669131645 670872323 676745206 4849437 SRX026482 SRS114569     Justus-Liebig University Giessen 1 0.9435   0.087   0.71429   0.46075   76   B   usable mapping rate illumina early_illumina unknown other unknown bulk unknown unknown   Germany 2011-03-31 Larval Larval Embryo Imprecise All anatomical structures

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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");;