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28 rows where experiment.library_selection = "size fractionation", technology = "unknown" and tissue_curation = "Trunk"

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devstage_curation 6

experiment.library_strategy 3

devstage_curation_coarse 3

experiment.platform 2

experiment.library_layout 2

tissue_curation_coarse 1

tissue_curation 1

  • Trunk · 28 ✖

technology 1

  • unknown · 28 ✖

experiment.library_source 1

experiment.library_selection 1

  • size fractionation · 28 ✖
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
36272 36272 SRR298567 SRX079845 SRS212651 SRP007331 PRJNA141525 Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish. GSE29418 Transcriptome Analysis RNA libraries from immunoprecipitates of Tdrd1 Ziwi and Zili total testis RNA total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.   pubmed:21743441   ZiliIPTes GSM727524   tissue:RNA obtained from immunoprecipitation with Zili antibody|strain:TL ZiliIPTes three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9. RNA obtained from immunoprecipitation with Zili antibody   Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 µl Dynabeads Invitrogen 3 or 6 testes and Zili antibody in a total volume of 500 µl. RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.   strain:TL GSM727524 GSM727524: ZiliIPTes GSM727524: ZiliIPTes GSM727524: ZiliIPTes 1   GEO Accession:GSM727524 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer II <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP007331   read name barcode proc directive:ignore ZiliIPTes.fastq fastq 995759064.0 27659974.0 GSM727524 1 0:36   36                 SRX079845 SRS212651 SRA039167 GEO European Research Institute for the Biology of Ageing, University Medical Center Groningen 1 0.0537   0.03117   0.95856   0.42091   36   B   usable mapping rate illumina early_illumina 5prime size_fractionation unknown bulk unknown unknown   Netherlands 2011-05-20 Undetermined Undetermined Trunk Surface Structure
36335 36335 SRR398322 SRX115580 SRS285697 SRP010291 PRJNA150927 miR 221 is required for endothelial tip cell behaviors during vascular development GSE35078 Transcriptome Analysis Through deep sequencing and functional screening in zebrafish we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor. Furthermore miR 221 was required for tip cell proliferation and migration as well as tip cell potential in mosaic blood vessels. miR 221 knockdown also prevented “hyper angiogenesis” defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling. Finally miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1. These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells.   pubmed:22340502   miRNA GFP minus GSM861784   source name:whole zebrafish embryos at 24 hpf|age:24 hpf|development stage:embryo|tissue:whole body|cell type:all cell types miRNA GFP minus The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2. whole zebrafish embryos at 24 hpf Tgkdrl:egfp embryos were dissociated at 24 hpf followed by fluorescence activated cell sorting to isolate GFP positive and negative cells. Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters followed by cDNA synthesis and amplification with Illumina primers.   age:24 hpf|developmental stage:embryo|tissue:whole body|cell type:all cell types GSM861784 GSM861784: miRNA GFP minus; Danio rerio; RNA Seq GSM861784 1 GSM861784: miRNA GFP minus 1   GEO Accession:GSM861784 RNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina Genome Analyzer <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</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></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> SRP010291     miRNA_CNTL_WT.fastq.gz fastq 295021332.0 8195037.0 GSM861784 r1 0:36 A:70414178;C:53495749;G:76994313;T:87833261;N:6283831 36       70414178 53495749 76994313 87833261 6283831 SRX115580 SRS285697 SRA049243 GEO Nathan Lawson Lab, PGFE, Umass Medical School 1 0.02832   0.02716   0.99957   0.43137   36   B   usable mapping rate illumina early_illumina unknown size_fractionation unknown bulk unknown unknown   United States 2012-01-12 Pharyngula Embryo Trunk Surface Structure
41250 41250 SRR3987432 SRX1989729 SRS1593551 SRP080353 PRJNA335856 High throughput sequencing analysis identify miRNAs in 7dpf F1 zebrafish under ß diketone antibiotics exposure to F0 zebrafish GSE85004 Transcriptome Analysis Small RNA high throughput sequencing technology was used to characterize the miRNAs in F1 zebrafish post 90 day ß diketone antibiotic DKA exposure to F0 zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7 dpf F1 zebrafish were constructed. In total 10 117 347 9 818 830 and 12 049 949 raw reads were acquired respectively under the different DKA exposure treatments 0 6.25 mg/L and 12.5mg/L from the three miRNAs libraries by Illumina sequencing. Low quality reads were removed which included five prime' contaminants those missing the three prime' primer or insert tag sequences with a poly A tail and those shorter than 17 nt and longer than 25 nt. As a result 8 141 146 representing 312 735 unique sequences; control 8 687 210 representing 251 508 unique sequences; 6.25 mg/L and 10 569 566 representing 441 938 unique sequences; 12.5 mg/L valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar and the unique sRNA reads were mainly distributed in the 20 24 nt range among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads respectively. The 22 nt sRNAs were the most abundant with the length distribution of counts of sequ seqs and unique miRNAs displaying a normal distribution. Overall design: Sample 1: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 12.5 mg/L.       S12 F1 GSM2255739   source name:F1 zebrafish 7 dpf F0 12.5 mg/L DKA exposure|strain/background:AB|genotype/variation:WT|f0 treatment:12.5 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf S12 F1 Briefly the raw reads were subjected to the Illumina pipeline filter Solexa 0.3 and then the dataset was further processed with an in house program ACGT101 miR LC Sciences Houston Texas USA to remove adapter dimers junk low complexity common RNA families rRNA tRNA snRNA snoRNA and repeats. Subsequently unique sequences with length in 1826 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 20.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software http://rna.tbi.univie.ac.at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem <=12; 2 number of base pairs in the stem region of the predicted hairpin >=16; 3 cutoff of free energy kCal/mol <=15; 4 length of hairpin up and down stems + terminal loop >=50; 5 length of hairpin loop <=20; 6 number of nucleotides in one bulge in mature region <=8; 7 number of biased errors in one bulge in mature region<=4; 8 number of biased bulges in mature region <=2; 9 number of errors in mature region <=7; 10 number of base pairs in the mature region of the … F1 zebrafish 7 dpf F0 12.5 mg/L DKA exposure Adult wild type zebrafish AB strain were purchased from a local supplier. Embryos at 6 hpf were exposed to control and two DKA treatments 6.25 and 12.5 mg/L composed of a mix of the six DKA species listed below with equal weight concentrations and equal volumes of each DKA species. post 90 days of DKA exposure F1 zebrafish at 7 dpf for each group control and two DKA exposure treatments were collected. Certified DKA reference standards were sourced from Amresco Solon OH USA and used as received: ofluoxacin CAS No. 82419 36 1 purity of 99% ciprofloxacin 85721 33 1 99% enrofloxacin 93106 60 6 99% doxycycline 24390 14 5 99% chlortetracycline 64 72 2 95% and oxytetracycline 79 57 2 99%. Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol.   strain/background:AB|genotype/variation:WT|f0 treatment:12.5 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf GSM2255739 GSM2255739: S12 F1; Danio rerio; ncRNA Seq GSM2255739   1 Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol. GEO Accession:GSM2255739 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP080353     S12_F1.fq fastq 602497450.0 12049949.0 GSM2255739 r1 0:50 A:147750395;C:138369661;G:162147841;T:153975593;N:253960 50       147750395 138369661 162147841 153975593 253960 SRX1989729 SRS1593551 SRA446490 GEO Wenzhou Medical University Chashan Campus Chashan University Town, Wenzhou, Zhejiang Province 1 0.0   0.0   1.0       50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2016-07-29 Larval Larval Trunk Surface Structure
41251 41251 SRR3987431 SRX1989728 SRS1593550 SRP080353 PRJNA335856 High throughput sequencing analysis identify miRNAs in 7dpf F1 zebrafish under ß diketone antibiotics exposure to F0 zebrafish GSE85004 Transcriptome Analysis Small RNA high throughput sequencing technology was used to characterize the miRNAs in F1 zebrafish post 90 day ß diketone antibiotic DKA exposure to F0 zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7 dpf F1 zebrafish were constructed. In total 10 117 347 9 818 830 and 12 049 949 raw reads were acquired respectively under the different DKA exposure treatments 0 6.25 mg/L and 12.5mg/L from the three miRNAs libraries by Illumina sequencing. Low quality reads were removed which included five prime' contaminants those missing the three prime' primer or insert tag sequences with a poly A tail and those shorter than 17 nt and longer than 25 nt. As a result 8 141 146 representing 312 735 unique sequences; control 8 687 210 representing 251 508 unique sequences; 6.25 mg/L and 10 569 566 representing 441 938 unique sequences; 12.5 mg/L valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar and the unique sRNA reads were mainly distributed in the 20 24 nt range among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads respectively. The 22 nt sRNAs were the most abundant with the length distribution of counts of sequ seqs and unique miRNAs displaying a normal distribution. Overall design: Sample 1: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 12.5 mg/L.       S6 F1 GSM2255738   source name:F1 zebrafish 7 dpf F0 6.25 mg/L DKA exposure|strain/background:AB|genotype/variation:WT|f0 treatment:6.25 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf S6 F1 Briefly the raw reads were subjected to the Illumina pipeline filter Solexa 0.3 and then the dataset was further processed with an in house program ACGT101 miR LC Sciences Houston Texas USA to remove adapter dimers junk low complexity common RNA families rRNA tRNA snRNA snoRNA and repeats. Subsequently unique sequences with length in 1826 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 20.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software http://rna.tbi.univie.ac.at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem <=12; 2 number of base pairs in the stem region of the predicted hairpin >=16; 3 cutoff of free energy kCal/mol <=15; 4 length of hairpin up and down stems + terminal loop >=50; 5 length of hairpin loop <=20; 6 number of nucleotides in one bulge in mature region <=8; 7 number of biased errors in one bulge in mature region<=4; 8 number of biased bulges in mature region <=2; 9 number of errors in mature region <=7; 10 number of base pairs in the mature region of the … F1 zebrafish 7 dpf F0 6.25 mg/L DKA exposure Adult wild type zebrafish AB strain were purchased from a local supplier. Embryos at 6 hpf were exposed to control and two DKA treatments 6.25 and 12.5 mg/L composed of a mix of the six DKA species listed below with equal weight concentrations and equal volumes of each DKA species. post 90 days of DKA exposure F1 zebrafish at 7 dpf for each group control and two DKA exposure treatments were collected. Certified DKA reference standards were sourced from Amresco Solon OH USA and used as received: ofluoxacin CAS No. 82419 36 1 purity of 99% ciprofloxacin 85721 33 1 99% enrofloxacin 93106 60 6 99% doxycycline 24390 14 5 99% chlortetracycline 64 72 2 95% and oxytetracycline 79 57 2 99%. Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol.   strain/background:AB|genotype/variation:WT|f0 treatment:6.25 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf GSM2255738 GSM2255738: S6 F1; Danio rerio; ncRNA Seq GSM2255738   1 Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol. GEO Accession:GSM2255738 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP080353     S6_F1.fq fastq 490941500.0 9818830.0 GSM2255738 r1 0:50 A:119942635;C:111532763;G:133144810;T:126303825;N:17467 50       119942635 111532763 133144810 126303825 17467 SRX1989728 SRS1593550 SRA446490 GEO Wenzhou Medical University Chashan Campus Chashan University Town, Wenzhou, Zhejiang Province 1 1e-05   0.0   1.0       50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2016-07-29 Larval Larval Trunk Surface Structure
41252 41252 SRR3987430 SRX1989727 SRS1593549 SRP080353 PRJNA335856 High throughput sequencing analysis identify miRNAs in 7dpf F1 zebrafish under ß diketone antibiotics exposure to F0 zebrafish GSE85004 Transcriptome Analysis Small RNA high throughput sequencing technology was used to characterize the miRNAs in F1 zebrafish post 90 day ß diketone antibiotic DKA exposure to F0 zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7 dpf F1 zebrafish were constructed. In total 10 117 347 9 818 830 and 12 049 949 raw reads were acquired respectively under the different DKA exposure treatments 0 6.25 mg/L and 12.5mg/L from the three miRNAs libraries by Illumina sequencing. Low quality reads were removed which included five prime' contaminants those missing the three prime' primer or insert tag sequences with a poly A tail and those shorter than 17 nt and longer than 25 nt. As a result 8 141 146 representing 312 735 unique sequences; control 8 687 210 representing 251 508 unique sequences; 6.25 mg/L and 10 569 566 representing 441 938 unique sequences; 12.5 mg/L valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar and the unique sRNA reads were mainly distributed in the 20 24 nt range among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads respectively. The 22 nt sRNAs were the most abundant with the length distribution of counts of sequ seqs and unique miRNAs displaying a normal distribution. Overall design: Sample 1: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 12.5 mg/L.       CON F1 GSM2255737   source name:F1 zebrafish 7 dpf F0 0 mg/L DKA exposure|strain/background:AB|genotype/variation:WT|f0 treatment:0 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf CON F1 Briefly the raw reads were subjected to the Illumina pipeline filter Solexa 0.3 and then the dataset was further processed with an in house program ACGT101 miR LC Sciences Houston Texas USA to remove adapter dimers junk low complexity common RNA families rRNA tRNA snRNA snoRNA and repeats. Subsequently unique sequences with length in 1826 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p and 5p derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 20.0 by BLAST search and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software http://rna.tbi.univie.ac.at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem <=12; 2 number of base pairs in the stem region of the predicted hairpin >=16; 3 cutoff of free energy kCal/mol <=15; 4 length of hairpin up and down stems + terminal loop >=50; 5 length of hairpin loop <=20; 6 number of nucleotides in one bulge in mature region <=8; 7 number of biased errors in one bulge in mature region<=4; 8 number of biased bulges in mature region <=2; 9 number of errors in mature region <=7; 10 number of base pairs in the mature region of the … F1 zebrafish 7 dpf F0 0 mg/L DKA exposure Adult wild type zebrafish AB strain were purchased from a local supplier. Embryos at 6 hpf were exposed to control and two DKA treatments 6.25 and 12.5 mg/L composed of a mix of the six DKA species listed below with equal weight concentrations and equal volumes of each DKA species. post 90 days of DKA exposure F1 zebrafish at 7 dpf for each group control and two DKA exposure treatments were collected. Certified DKA reference standards were sourced from Amresco Solon OH USA and used as received: ofluoxacin CAS No. 82419 36 1 purity of 99% ciprofloxacin 85721 33 1 99% enrofloxacin 93106 60 6 99% doxycycline 24390 14 5 99% chlortetracycline 64 72 2 95% and oxytetracycline 79 57 2 99%. Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol.   strain/background:AB|genotype/variation:WT|f0 treatment:0 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf GSM2255737 GSM2255737: CON F1; Danio rerio; ncRNA Seq GSM2255737   1 Total RNA was extracted using Trizol reagent Invitrogen CA USA following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent CA USA with RIN number >7.0. Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina San Diego USA. Then we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou China following the vendor’s recommended protocol. GEO Accession:GSM2255737 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP080353     CON_F1.fq fastq 505867350.0 10117347.0 GSM2255737 r1 0:50 A:123471791;C:114424623;G:138931875;T:129020913;N:18148 50       123471791 114424623 138931875 129020913 18148 SRX1989727 SRS1593549 SRA446490 GEO Wenzhou Medical University Chashan Campus Chashan University Town, Wenzhou, Zhejiang Province 1 2e-05   0.0   0.99993   0.66666   50   T   under 1.2% mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2016-07-29 Larval Larval Trunk Surface Structure
48627 48627 SRR7280654 SRX4184228 SRS3395608 SRP149913 PRJNA474911 Origin and Evolution of Neural Microexons PRJNA474911 Other Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain     Pool of one hundred 2hpf embryos 2hpf embryos Embr 2hpf   strain:AB|dev stage:2hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: 2hpf embryos Embr 2hpf Embr 2hpf RNA extracted from a pool of one hundred embryos     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500   SRP149913     Embr_2hpf_R2-125.fq.gz Embr_2hpf_R1-125.fq.gz fastq fastq 17109578000.0 68438312.0 Embr 2hpf R1 125.fq.gz 0:125 1:125 A:4536550134;C:4009266695;G:4076560218;T:4484964079;N:2236874 125 125     4536550134 4009266695 4076560218 4484964079 2236874 SRX4184228 SRS3395608 SRA717220 Centre for Genomic Regulation|Systems Biology Department Centre for Genomic Regulation 2 0.96221 0.96458 0.02765 0.02716 0.77116 0.77325 0.48649 0.4853 125 125 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2019-01-22 Cleavage Embryo Trunk Surface Structure
48628 48628 SRR7280655 SRX4184227 SRS3395607 SRP149913 PRJNA474911 Origin and Evolution of Neural Microexons PRJNA474911 Other Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain     Pool of one hundred 8hpf embryos 8hpf embryos Embr 8hpf   strain:AB|dev stage:8hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: 8hpf embryos Embr 8hpf Embr 8hpf RNA extracted from a pool of one hundred embryos     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500   SRP149913     Embr_8hpf_R1-125.fq.gz Embr_8hpf_R2-125.fq.gz fastq fastq 20486524750.0 81946099.0 Embr 8hpf R2 125.fq.gz 0:125 1:125 A:5437735333;C:4808439456;G:4859422420;T:5377132981;N:3794560 125 125     5437735333 4808439456 4859422420 5377132981 3794560 SRX4184227 SRS3395607 SRA717220 Centre for Genomic Regulation|Systems Biology Department Centre for Genomic Regulation 2 0.96373 0.95763 0.07096 0.0702 0.75937 0.75866 0.48455 0.484 125 125 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2019-01-22 Gastrula Embryo Trunk Surface Structure
48629 48629 SRR7280656 SRX4184226 SRS3395606 SRP149913 PRJNA474911 Origin and Evolution of Neural Microexons PRJNA474911 Other Our study focuses on the origin of the neural microexon program.We discover that neural microexon programs are present in non vertebrate speciesand trace their origin to bilaterian ancestors through the emergenceof a previously uncharacterized "enhancer of microexon" eMIC protein domain     Pool of one hundred 12hpf embryos 12hpf embryos Embr 12hpf   strain:AB|dev stage:12hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal                 RNA seq of Danio rerio: 12hpf embryos Embr 12hpf Embr 12hpf RNA extracted from a pool of one hundred embryos     RNA-Seq TRANSCRIPTOMIC size fractionation PAIRED ILLUMINA Illumina HiSeq 2500   SRP149913     Embr_12hpf_R2-125.fq.gz Embr_12hpf_R1-125.fq.gz fastq fastq 22366284500.0 89465138.0 Embr 12hpf R1 125.fq.gz 0:125 1:125 A:5886492098;C:5284016845;G:5382041408;T:5809628253;N:4105896 125 125     5886492098 5284016845 5382041408 5809628253 4105896 SRX4184226 SRS3395606 SRA717220 Centre for Genomic Regulation|Systems Biology Department Centre for Genomic Regulation 2 0.96226 0.96763 0.06393 0.06451 0.74355 0.74472 0.48233 0.48387 125 125 B B biological fallback assumption illumina hiseq_era unknown size_fractionation unknown bulk unknown unknown   Spain 2019-01-22 Segmentation Embryo Trunk Surface Structure
61688 61688 SRR13302966 SRX9731824 SRS7924603 SRP290217 PRJNA673345 Zebrafish as an animal model for the antiviral RNA interference pathway GSE160475 Transcriptome Analysis We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV vesicular stomatitis virus VSV and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs the hallmark of antiviral RNAi with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile the suppressor of RNAi VSR protein NoV B2 may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.       NoV△B2: Ago2 IP 3 dpi GSM4988099   source name:zebrafish whole body|zebrafish background:AB|infection:NoV△B2|injection way:microinjection|tissue:zebrafish whole body NoV△B2: Ago2 IP 3 dpi Sequenced reads were trimmed for adaptor sequence then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2 zebrafish whole body   Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.   zebrafish background:AB|infection:NoV△B2|injection way:microinjection|tissue:zebrafish whole body GSM4988099 GSM4988099: NoV△B2: Ago2 IP 3 dpi; Danio rerio; ncRNA Seq GSM4988099   1 Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA. GEO Accession:GSM4988099 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP290217     LY272.fq.gz fastq 2608504950.0 17390033.0 GSM4988099 r1 0:150 1:0 A:741941121;C:669191911;G:747181676;T:450096994;N:93248 150 0     741941121 669191911 747181676 450096994 93248 SRX9731824 SRS7924603 SRA1151114 GEO Fudan University 1 0.13133   0.03425   0.96802   0.60095   150   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2020-12-24 Undetermined Larval Trunk Surface Structure
61689 61689 SRR12951276 SRX9404383 SRS7622158 SRP290217 PRJNA673345 Zebrafish as an animal model for the antiviral RNA interference pathway GSE160475 Transcriptome Analysis We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV vesicular stomatitis virus VSV and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs the hallmark of antiviral RNAi with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile the suppressor of RNAi VSR protein NoV B2 may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.       SINV: zebrafish 3 dpi GSM4873784   source name:zebrafish whole body|tissue:whole body|infection:SINV|injection way:microinjection|zebrafish background:AB SINV: zebrafish 3 dpi Sequenced reads were trimmed for adaptor sequence then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2 zebrafish whole body   Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.   tissue:whole body|infection:SINV|injection way:microinjection|zebrafish background:AB GSM4873784 GSM4873784: SINV: zebrafish 3 dpi; Danio rerio; ncRNA Seq GSM4873784   1 Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA. GEO Accession:GSM4873784 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2000   SRP290217     4_LY215.fq.gz fastq 1328044600.0 26560892.0 GSM4873784 r1 0:50 1:0 A:383401484;C:303337306;G:339848340;T:301397824;N:59646 50 0     383401484 303337306 339848340 301397824 59646 SRX9404383 SRS7622158 SRA1151114 GEO Fudan University 1 0.83242   0.11559   0.93634   0.53516   50   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2020-10-30 Undetermined Larval Trunk Surface Structure
61690 61690 SRR12951275 SRX9404382 SRS7622159 SRP290217 PRJNA673345 Zebrafish as an animal model for the antiviral RNA interference pathway GSE160475 Transcriptome Analysis We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV vesicular stomatitis virus VSV and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs the hallmark of antiviral RNAi with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile the suppressor of RNAi VSR protein NoV B2 may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.       VSV: zebrafish 24 hpi GSM4873783   source name:zebrafish whole body|tissue:whole body|infection:VSV|injection way:microinjection|zebrafish background:AB VSV: zebrafish 24 hpi Sequenced reads were trimmed for adaptor sequence then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2 zebrafish whole body   Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.   tissue:whole body|infection:VSV|injection way:microinjection|zebrafish background:AB GSM4873783 GSM4873783: VSV: zebrafish 24 hpi; Danio rerio; ncRNA Seq GSM4873783   1 Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA. GEO Accession:GSM4873783 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP290217     3_LY157.fq.gz fastq 706147852.0 29418915.0 GSM4873783 r1 0:24.00 1:0 A:151681768;C:131117267;G:189016204;T:234316361;N:16252 24 0     151681768 131117267 189016204 234316361 16252 SRX9404382 SRS7622159 SRA1151114 GEO Fudan University 1 0.92973   0.12628   0.90664   0.45104   23   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2020-10-30 Undetermined Larval Trunk Surface Structure
61691 61691 SRR12951274 SRX9404381 SRS7622157 SRP290217 PRJNA673345 Zebrafish as an animal model for the antiviral RNA interference pathway GSE160475 Transcriptome Analysis We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV vesicular stomatitis virus VSV and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs the hallmark of antiviral RNAi with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile the suppressor of RNAi VSR protein NoV B2 may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.       NoV△B2: zebrafish 24 hpi GSM4873782   source name:zebrafish whole body|tissue:whole body|infection:NoV{delta}B2|injection way:microinjection|zebrafish background:AB NoV△B2: zebrafish 24 hpi Sequenced reads were trimmed for adaptor sequence then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2 zebrafish whole body   Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.   tissue:whole body|infection:NoV{delta}B2|injection way:microinjection|zebrafish background:AB GSM4873782 GSM4873782: NoV△B2: zebrafish 24 hpi; Danio rerio; ncRNA Seq GSM4873782   1 Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA. GEO Accession:GSM4873782 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP290217     2_LY156.fq.gz fastq 748544818.0 30779865.0 GSM4873782 r1 0:24.32 1:0 A:166631198;C:138321792;G:208615021;T:234953337;N:23470 24 0     166631198 138321792 208615021 234953337 23470 SRX9404381 SRS7622157 SRA1151114 GEO Fudan University 1 0.94115   0.12368   0.91076   0.48684   23   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2020-10-30 Undetermined Larval Trunk Surface Structure
61692 61692 SRR12951273 SRX9404380 SRS7622156 SRP290217 PRJNA673345 Zebrafish as an animal model for the antiviral RNA interference pathway GSE160475 Transcriptome Analysis We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV vesicular stomatitis virus VSV and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs the hallmark of antiviral RNAi with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile the suppressor of RNAi VSR protein NoV B2 may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.       NoV: zebrafish 24 hpi GSM4873781   source name:zebrafish whole body|tissue:whole body|infection:NoV|injection way:microinjection|zebrafish background:AB NoV: zebrafish 24 hpi Sequenced reads were trimmed for adaptor sequence then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2 zebrafish whole body   Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.   tissue:whole body|infection:NoV|injection way:microinjection|zebrafish background:AB GSM4873781 GSM4873781: NoV: zebrafish 24 hpi; Danio rerio; ncRNA Seq GSM4873781   1 Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA. GEO Accession:GSM4873781 ncRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE ILLUMINA Illumina HiSeq 2500   SRP290217     1_LY155.fq.gz fastq 594676353.0 25019145.0 GSM4873781 r1 0:23.77 1:0 A:129139705;C:108465388;G:162500636;T:194556532;N:14092 23 0     129139705 108465388 162500636 194556532 14092 SRX9404380 SRS7622156 SRA1151114 GEO Fudan University 1 0.93471   0.10892   0.90814   0.48797   22   B   usable mapping rate illumina hiseq_era unknown size_fractionation trueseq bulk unknown unknown   China 2020-10-30 Undetermined Larval Trunk Surface Structure
71643 71643 SRR21869762 SRX17856938 SRS15377982 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         BHEE H 3   replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 15|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221124 AT20221124 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py BHEE_H_3.fq.gz fastq 533428889.0 23211223.0 BHEE H 3.fq.gz 0:22.98 A:120057830;C:104713991;G:142506271;T:166150296;N:501 22       120057830 104713991 142506271 166150296 501 SRX17856938 SRS15377982 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.79272   0.10596   0.92431   0.52918   22   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71644 71644 SRR21869763 SRX17856937 SRS15377981 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         BHEE H 2   replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 14|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221123 AT20221123 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py BHEE_H_2.fq.gz fastq 542237520.0 23757627.0 BHEE H 2.fq.gz 0:22.82 A:118608004;C:107602147;G:146341292;T:169685803;N:274 22       118608004 107602147 146341292 169685803 274 SRX17856937 SRS15377981 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.78829   0.10064   0.91346   0.52625   22   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71645 71645 SRR21869764 SRX17856936 SRS15377980 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         BHEE H 1   replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 13|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221122 AT20221122 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py BHEE_H_1.fq.gz fastq 553437966.0 24068768.0 BHEE H 1.fq.gz 0:22.99 A:123764056;C:109954264;G:151884637;T:167834745;N:264 22       123764056 109954264 151884637 167834745 264 SRX17856936 SRS15377980 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.70849   0.09465   0.91768   0.52194   22   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71646 71646 SRR21869765 SRX17856935 SRS15377979 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         BHEE L 3   replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 12|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221121 AT20221121 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py BHEE_L_3.fq.gz fastq 534633614.0 23823089.0 BHEE L 3.fq.gz 0:22.44 A:117363754;C:102332510;G:134833529;T:180103711;N:110 22       117363754 102332510 134833529 180103711 110 SRX17856935 SRS15377979 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.91988   0.08325   0.94073   0.53253   23   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71647 71647 SRR21869766 SRX17856934 SRS15377978 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         BHEE L 2   replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 11|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221120 AT20221120 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py BHEE_L_2.fq.gz fastq 544854900.0 24226737.0 BHEE L 2.fq.gz 0:22.49 A:119782823;C:104902871;G:136756907;T:183412172;N:127 22       119782823 104902871 136756907 183412172 127 SRX17856934 SRS15377978 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.93474   0.08179   0.9345   0.52916   22   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71648 71648 SRR21869767 SRX17856933 SRS15377990 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         BHEE L 1   replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 10|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221119 AT20221119 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py BHEE_L_1.fq.gz fastq 536871966.0 23768969.0 BHEE L 1.fq.gz 0:22.59 A:117321330;C:102381550;G:133641788;T:183527144;N:154 22       117321330 102381550 133641788 183527144 154 SRX17856933 SRS15377990 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.94042   0.08986   0.93141   0.51821   22   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71649 71649 SRR21869768 SRX17856932 SRS15377989 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         TBBPA H 3   replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 9|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221118 AT20221118 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py TBBPA_H_3.fq.gz fastq 528430937.0 23464221.0 TBBPA H 3.fq.gz 0:22.52 A:115261465;C:101477007;G:136961367;T:174730904;N:194 22       115261465 101477007 136961367 174730904 194 SRX17856932 SRS15377989 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.89616   0.09929   0.93042   0.5004   22   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71650 71650 SRR21869769 SRX17856931 SRS15377988 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         TBBPA H 2   replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 8|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221117 AT20221117 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py TBBPA_H_2.fq.gz fastq 523343500.0 22888420.0 TBBPA H 2.fq.gz 0:22.86 A:114272050;C:101352294;G:133914155;T:173804699;N:302 22       114272050 101352294 133914155 173804699 302 SRX17856931 SRS15377988 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.90842   0.10759   0.92088   0.53284   20   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71651 71651 SRR21869770 SRX17856930 SRS15377987 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         TBBPA H 1   replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 7|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221116 AT20221116 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py TBBPA_H_1.fq.gz fastq 538481195.0 23517366.0 TBBPA H 1.fq.gz 0:22.90 A:117132485;C:106262580;G:143962997;T:171122739;N:394 22       117132485 106262580 143962997 171122739 394 SRX17856930 SRS15377987 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.83673   0.10787   0.91238   0.53365   21   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71652 71652 SRR21869771 SRX17856929 SRS15377986 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         TBBPA L 3   replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 6|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221115 AT20221115 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py TBBPA_L_3.fq.gz fastq 536529124.0 23817957.0 TBBPA L 3.fq.gz 0:22.53 A:115664153;C:104457844;G:136444705;T:179962303;N:119 22       115664153 104457844 136444705 179962303 119 SRX17856929 SRS15377986 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.86178   0.09041   0.93624   0.4992   22   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71654 71654 SRR21869773 SRX17856927 SRS15377985 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         TBBPA L 2   replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 5|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221114 AT20221114 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py TBBPA_L_2.fq.gz fastq 525712427.0 23458446.0 TBBPA L 2.fq.gz 0:22.41 A:115172158;C:103930973;G:133832634;T:172776555;N:107 22       115172158 103930973 133832634 172776555 107 SRX17856927 SRS15377985 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.87223   0.08526   0.93845   0.54116   22   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71655 71655 SRR21869774 SRX17856926 SRS15377984 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         TBBPA L 1   replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 4|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221113 AT20221113 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py TBBPA_L_1.fq.gz fastq 527804519.0 23370082.0 TBBPA L 1.fq.gz 0:22.58 A:114266025;C:102477479;G:134403120;T:176657729;N:166 22       114266025 102477479 134403120 176657729 166 SRX17856926 SRS15377984 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.89339   0.09635   0.92608   0.48415   22   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71656 71656 SRR21869775 SRX17856925 SRS15377983 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         Control 3   replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 3|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221112 AT20221112 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py Control_3.fq.gz fastq 535579212.0 23899710.0 Control 3.fq.gz 0:22.41 A:117125157;C:106586085;G:133001456;T:178866289;N:225 22       117125157 106586085 133001456 178866289 225 SRX17856925 SRS15377983 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.89094   0.06851   0.94807   0.54835   23   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71657 71657 SRR21869776 SRX17856924 SRS15377977 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         Control 2   replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 2|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221111 AT20221111 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py Control_2.fq.gz fastq 528466892.0 23430674.0 Control 2.fq.gz 0:22.55 A:116361274;C:103960709;G:132758802;T:175385846;N:261 22       116361274 103960709 132758802 175385846 261 SRX17856924 SRS15377977 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.89063   0.07453   0.94255   0.54503   21   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure
71658 71658 SRR21869777 SRX17856923 SRS15377976 SRP402080 PRJNA889683 miRNA mRNA sequencing of zebrafish embryos PRJNA889683 Other miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE         Control 1   replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 1|BioSampleModel:Model organism or animal                 miRNA Seq of zebrafish larvae AT20221110 AT20221110 miRNA Seq of zebrafish larvae     miRNA-Seq TRANSCRIPTOMIC size fractionation SINGLE BGISEQ BGISEQ-500   SRP402080   loader:fastq load.py Control_1.fq.gz fastq 517484481.0 23046792.0 Control 1.fq.gz 0:22.45 A:114187486;C:101456491;G:129311971;T:172528320;N:213 22       114187486 101456491 129311971 172528320 213 SRX17856923 SRS15377976 SRA1518395 Jiangsu University|School of Environment and Safety Engineering Jiangsu University 1 0.89811   0.07533   0.93198   0.55322   22   B   usable mapping rate bgi bgi unknown size_fractionation unknown bulk unknown unknown   China 2022-10-12 Larval Larval Trunk Surface Structure

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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;