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RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "M1l_R2.fq.gz M1l_R1.fq.gz", "fastq fastq", 8301268800.0, 27670896.0, "M1l R1.fq.gz", "0:150 1:150", "A:1856070257;C:2266693166;G:2413641098;T:1764769457;N:94822", 150, 150, null, null, 1856070257, 2266693166, 2413641098, 1764769457, 94822, "SRX25008881", "SRS21709100", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.8289, 0.73852, 0.21964, 0.50932, 0.99648, 0.99701, 0.57332, 0.51129, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32928, "SRR29498572", "SRX25008880", "SRS21709099", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "M1b", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:brain|identifier:M1b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "05", "05", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "M1b_R1.fq.gz M1b_R2.fq.gz", "fastq fastq", 7947472800.0, 26491576.0, "M1b R1.fq.gz", "0:150 1:150", "A:1764190500;C:1937842699;G:2595509352;T:1649839967;N:90282", 150, 150, null, null, 1764190500, 1937842699, 2595509352, 1649839967, 90282, "SRX25008880", "SRS21709099", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.96542, 0.21476, 0.17288, 0.05982, 0.97289, 0.99711, 0.57845, 0.611, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Brain", "Nervous System"], [32929, "SRR29498573", "SRX25008879", "SRS21709098", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "F2l", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:liver|identifier:F2l|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "04", "04", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "F2l_R1.fq.gz F2l_R2.fq.gz", "fastq fastq", 8701893900.0, 29006313.0, "F2l R1.fq.gz", "0:150 1:150", "A:1977580339;C:2299061131;G:2585058451;T:1840095650;N:98329", 150, 150, null, null, 1977580339, 2299061131, 2585058451, 1840095650, 98329, "SRX25008879", "SRS21709098", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.72425, 0.57704, 0.15111, 0.37121, 0.99744, 0.99762, 0.61161, 0.55762, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32930, "SRR29498574", "SRX25008878", "SRS21709097", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "F2b", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:brain|identifier:F2b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "03", "03", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "F2b_R1.fq.gz F2b_R2.fq.gz", "fastq fastq", 9249410100.0, 30831367.0, "F2b R1.fq.gz", "0:150 1:150", "A:2101671138;C:2272479255;G:2931272789;T:1943881150;N:105768", 150, 150, null, null, 2101671138, 2272479255, 2931272789, 1943881150, 105768, "SRX25008878", "SRS21709097", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.96654, 0.19343, 0.23127, 0.08081, 0.95272, 0.99326, 0.63762, 0.64901, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Brain", "Nervous System"], [32931, "SRR29498575", "SRX25008877", "SRS21709096", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "M2g", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:gut|identifier:M2g|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "12", "12", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "M2g_R1.fq.gz M2g_R2.fq.gz", "fastq fastq", 7106243100.0, 23687477.0, "M2g R1.fq.gz", "0:150 1:150", "A:1567154123;C:1866065312;G:2213286944;T:1459656676;N:80045", 150, 150, null, null, 1567154123, 1866065312, 2213286944, 1459656676, 80045, "SRX25008877", "SRS21709096", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.56476, 0.25026, 0.02259, 0.04481, 0.99667, 0.99701, 0.63277, 0.65693, 150, 150, "B", "B", "mate2-mate1 similar by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Gut", "Digestive System"], [32932, "SRR29498576", "SRX25008876", "SRS21709095", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "M1g", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:male|tissue:gut|identifier:M1g|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "11", "11", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "M1g_R2.fq.gz M1g_R1.fq.gz", "fastq fastq", 7351182000.0, 24503940.0, "M1g R1.fq.gz", "0:150 1:150", "A:1623685246;C:1858847576;G:2315396486;T:1553169371;N:83321", 150, 150, null, null, 1623685246, 1858847576, 2315396486, 1553169371, 83321, "SRX25008876", "SRS21709095", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.96004, 0.21521, 0.16113, 0.04578, 0.92431, 0.99143, 0.61867, 0.63432, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Gut", "Digestive System"], [32933, "SRR29498577", "SRX25008875", "SRS21709094", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "F1l", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:liver|identifier:F1l|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "02", "02", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "F1l_R2.fq.gz F1l_R1.fq.gz", "fastq fastq", 4647564000.0, 15491880.0, "F1l R1.fq.gz", "0:150 1:150", "A:993332389;C:862184908;G:1814249126;T:977710185;N:87392", 150, 150, null, null, 993332389, 862184908, 1814249126, 977710185, 87392, "SRX25008875", "SRS21709094", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.88683, 0.14922, 0.24654, 0.08178, 0.9583, 0.99819, 0.70978, 0.20254, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Liver", "Liver and Biliary System"], [32934, "SRR29498578", "SRX25008874", "SRS21709093", "SRP515416", "PRJNA1127032", "Zebrafish Tissue Mid Range RNA Sequencing", "PRJNA1127032", "Other", "This project sequenced mid size ranged RNA from zebrafish liver  brain  and gut tissues  using male and female parallel samples.", null, null, null, null, "F1b", null, "strain:AB|age:adult|dev stage:adult|collection date:2020|geo loc name:Hungary|sex:female|tissue:brain|identifier:F1b|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "midRNA seq Danio rerio", "01", "01", "Total RNA was extracted from different zebrafish tissues  using TRIzol reagent. RNA purity can be assesed by genomic DNA contamination minimized using DNase I and RNA Clean Up kit. post size selection our samples were sequenced with Illumina technology.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP515416", null, null, "F1b_R2.fq.gz F1b_R1.fq.gz", "fastq fastq", 7995852300.0, 26652841.0, "F1b R1.fq.gz", "0:150 1:150", "A:1744452113;C:2053788787;G:2580416325;T:1617104387;N:90688", 150, 150, null, null, 1744452113, 2053788787, 2580416325, 1617104387, 90688, "SRX25008874", "SRS21709093", "SRA1905460", "Eotvos Lorand University|Genetics", "Eotvos Lorand University", 2, 0.96107, 0.17798, 0.16452, 0.02921, 0.96759, 0.99677, 0.66455, 0.62672, 150, 150, "B", "T", "mate2 technical by mapping diff", "illumina", "novaseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Hungary", "2024-06-22", "Adult", "Adult", "Brain", "Nervous System"], [40707, "SRR3502888", "SRX1760541", "SRS1436386", "SRP072296", "PRJNA316313", "Codon optimality and mRNA decay in zebrafish and Xenopus", "PRJNA316313", "Other", "Cellular transitions require dramatic changes in gene expression that are supported by regulated mRNA decay and new transcription. The maternal to zygotic transition is a conserved developmental progression during which thousands of maternal mRNAs are cleared by posttranscriptional mechanisms. Although some maternal mRNAs are targeted for degradation by microRNAs  this pathway does not fully explain mRNA clearance. Because the ribosome constitutes the main ribonucleoprotein complex decoding the mRNA  we investigated how codon identity and translation affect mRNA stability during development and homeostasis. Using an in vivo selection strategy  we show that the codon triplet contains translation dependent regulatory information that influences transcript decay. We find that codon composition shapes maternal mRNA clearance during the maternal to zygotic transition in zebrafish  Xenopus  mouse and Drosophila  and gene expression during homeostasis across human tissues. Codon composition affects both polyadenylation status and translation efficiency. Thus  the ribosome interprets two codes within the mRNA  the genetic code which specifies the amino acid sequence  and a conserved \u201ccodon optimality code\u201d that shapes mRNA stability and translation efficiency across vertebrates.", null, null, null, "Zebrafish tRNA at 6hpf", "tRNA AB 6h", null, "strain:TUAB|age:6hpf|dev stage:Shield|sex:pooled male and female|tissue:Whole animal|collected by:Ariel Bazzini|genotype:WT|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Zebrafish tRNAs at 6hpf", "tRNA 6hpf zebrafish", "TGIRT tRNA Library", "1", null, null, "OTHER", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>152</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>77</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP072296", null, null, "AB-tRNA_S9_R1_001.fastq.gz AB-tRNA_S9_R2_001.fastq.gz", "fastq fastq", 7860522000.0, 26201740.0, "tRNA zebrafish 6hpf", "0:150 1:150", "A:1945184302;C:2012637521;G:2171934357;T:1730625218;N:140602", 150, 150, null, null, 1945184302, 2012637521, 2171934357, 1730625218, 140602, "SRX1760541", "SRS1436386", "SRA395141", "Yale University|Giraldez Lab", "Yale University", 2, 0.04186, 0.04313, 0.00633, 0.00639, 0.96834, 0.96913, 0.53967, 0.5329, 150, 150, "T", "T", "mates < 9% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2016-06-17", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [41348, "SRR4302022", "SRX2194190", "SRS1716514", "SRP090540", "PRJNA344550", "Danio rerio strain:AB Raw sequence reads", "PRJNA344550", "Whole Genome Sequencing", "Identification of circular RNAs in zebrafish", null, "pubmed:27878987", null, null, "Zebrafish circRNA", null, "strain:AB|age:Adult|sex:pooled male and female|tissue:brain  eyes  heart  liver  spleen  kidney  intestines  skin  muscle  gill  ovary  testis|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Identification of circular RNAs in zebrafish", "Zebrafish circRNAs", "Key Lab of Agricultural Animal Genetics", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</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>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP090540", null, null, "MIX_R1.fastq.gz MIX_R2.fastq.gz", "fastq fastq", 21319208400.0, 71064028.0, "Zebrafish circRNAs", "0:150 1:150", "A:4973737880;C:5734846860;G:5920594296;T:4689011877;N:1017487", 150, 150, null, null, 4973737880, 5734846860, 5920594296, 4689011877, 1017487, "SRX2194190", "SRS1716514", "SRA480645", "Huazhong Agricultural University|Key Lab of Agricultural Animal Genetics", "Huazhong Agricultural University", 2, 0.89959, 0.92292, 0.28429, 0.27588, 0.87207, 0.86866, 0.65238, 0.78485, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2016-11-28", "Adult", "Adult", "Multi-tissue", "Multi-system"], [42495, "SRR5666979", "SRX2902577", "SRS2269173", "SRP108989", "PRJNA390119", "HLX & Hematopoiesis", "PRJNA390119", "Other", "HLX &amp; Hematopoiesis", null, null, "rnaseq and atacseq", "hlx hematopoiesis", "hlx", null, "isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "kdrl GFP cells hlx1  MO rep2", "3", "kdrl GFP cells hlx1  MO rep2", "SMART SEQ ultra low RNA seq kit Clonetech", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP108989", null, "assembly:danRer10", "flk_gfp_hlx_8ng_48hrs_2_R1.fastq.gz flk_gfp_hlx_8ng_48hrs_2_R2.fastq.gz", "fastq fastq", 1887289200.0, 12581928.0, "flk gfp hlx 8ng 48hrs 2 R1.fastq.gz", "0:75 1:75", "A:493825524;C:448630716;G:436118597;T:508410442;N:303921", 75, 75, null, null, 493825524, 448630716, 436118597, 508410442, 303921, "SRX2902577", "SRS2269173", "SRA573518", "BRFAA|Molecular Biology", "BRFAA", 2, 0.9202, 0.9216, 0.09499, 0.09558, 0.73805, 0.73878, 0.48809, 0.48787, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Greece", "2017-06-13", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [42496, "SRR5666980", "SRX2902576", "SRS2269173", "SRP108989", "PRJNA390119", "HLX & Hematopoiesis", "PRJNA390119", "Other", "HLX &amp; Hematopoiesis", null, null, "rnaseq and atacseq", "hlx hematopoiesis", "hlx", null, "isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "kdrl GFP cells hlx1  MO rep1", "2", "kdrl GFP cells hlx1  MO rep1", "SMART SEQ ultra low RNA seq kit Clonetech", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP108989", null, "assembly:danRer10", "flk_gfp_hlx_8ng_48hrs_1_R1.fastq.gz flk_gfp_hlx_8ng_48hrs_1_R2.fastq.gz", "fastq fastq", 1561083900.0, 10407226.0, "flk gfp hlx 8ng 48hrs 1 R2.fastq.gz", "0:75 1:75", "A:412744284;C:366776465;G:356834742;T:424473871;N:254538", 75, 75, null, null, 412744284, 366776465, 356834742, 424473871, 254538, "SRX2902576", "SRS2269173", "SRA573518", "BRFAA|Molecular Biology", "BRFAA", 2, 0.9172, 0.91824, 0.09957, 0.09961, 0.73965, 0.73975, 0.48906, 0.48977, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Greece", "2017-06-13", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [42497, "SRR5666981", "SRX2902575", "SRS2269173", "SRP108989", "PRJNA390119", "HLX & Hematopoiesis", "PRJNA390119", "Other", "HLX &amp; Hematopoiesis", null, null, "rnaseq and atacseq", "hlx hematopoiesis", "hlx", null, "isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "kdrl GFP cells control 2", "1", "kdrl GFP cells control 2", "SMART SEQ ultra low RNA seq kit Clonetech", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP108989", null, "assembly:danRer10", "flk_gfp_48hrs_con2_R1.fastq.gz flk_gfp_48hrs_con2_R2.fastq.gz", "fastq fastq", 2042164500.0, 13614430.0, "flk gfp 48hrs con2 R1.fastq.gz", "0:75 1:75", "A:537008617;C:483956616;G:465380092;T:555490621;N:328554", 75, 75, null, null, 537008617, 483956616, 465380092, 555490621, 328554, "SRX2902575", "SRS2269173", "SRA573518", "BRFAA|Molecular Biology", "BRFAA", 2, 0.91492, 0.91762, 0.10575, 0.10669, 0.75519, 0.75546, 0.49482, 0.49617, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Greece", "2017-06-13", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [42498, "SRR5666982", "SRX2902574", "SRS2269173", "SRP108989", "PRJNA390119", "HLX & Hematopoiesis", "PRJNA390119", "Other", "HLX &amp; Hematopoiesis", null, null, "rnaseq and atacseq", "hlx hematopoiesis", "hlx", null, "isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "kdrl GFP cells control 1", "0", "kdrl GFP cells control 1", "SMART SEQ ultra low RNA seq kit Clonetech", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP108989", null, "assembly:danRer10", "flk_gfp_48hrs_con1_R2.fastq.gz flk_gfp_48hrs_con1_R1.fastq.gz", "fastq fastq", 1678987200.0, 11193248.0, "flk gfp 48hrs con1 R2.fastq.gz", "0:75 1:75", "A:437283407;C:401234553;G:387947515;T:452257282;N:264443", 75, 75, null, null, 437283407, 401234553, 387947515, 452257282, 264443, "SRX2902574", "SRS2269173", "SRA573518", "BRFAA|Molecular Biology", "BRFAA", 2, 0.91593, 0.91737, 0.08937, 0.08988, 0.75607, 0.75696, 0.50103, 0.45539, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Greece", "2017-06-13", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [42499, "SRR5666985", "SRX2902571", "SRS2269173", "SRP108989", "PRJNA390119", "HLX & Hematopoiesis", "PRJNA390119", "Other", "HLX &amp; Hematopoiesis", null, null, "rnaseq and atacseq", "hlx hematopoiesis", "hlx", null, "isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "fli GFP cells hHLXOE rep 2", "5", "fli GFP cells hHLXOE rep 2", "SMART SEQ ultra low RNA seq kit Clonetech", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP108989", null, "assembly:danRer10", "fli_gal4_uas_hlx_endo_48h_s2_R2.fastq.gz fli_gal4_uas_hlx_endo_48h_s2_R1.fastq.gz", "fastq fastq", 4490898450.0, 29939323.0, "fli gal4 uas hlx endo 48h s2 R2.fastq.gz", "0:75 1:75", "A:870349076;C:1346136891;G:1401796534;T:869066463;N:3549486", 75, 75, null, null, 870349076, 1346136891, 1401796534, 869066463, 3549486, "SRX2902571", "SRS2269173", "SRA573518", "BRFAA|Molecular Biology", "BRFAA", 2, 0.5714, 0.57344, 0.27957, 0.28321, 0.85102, 0.85342, 0.53304, 0.53368, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Greece", "2017-06-13", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [42500, "SRR5666986", "SRX2902570", "SRS2269173", "SRP108989", "PRJNA390119", "HLX & Hematopoiesis", "PRJNA390119", "Other", "HLX &amp; Hematopoiesis", null, null, "rnaseq and atacseq", "hlx hematopoiesis", "hlx", null, "isolate:multiisolates|age:N/A|sex:pooled male and female|tissue:heart|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "fli GFP cells hHLXOE rep 1", "4", "fli GFP cells hHLXOE rep 1", "SMART SEQ ultra low RNA seq kit Clonetech", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>150</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>76</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP108989", null, "assembly:danRer10", "fli_gal4_uas_hlx_endo_48h_s1_R1.fastq.gz fli_gal4_uas_hlx_endo_48h_s1_R2.fastq.gz", "fastq fastq", 3459602100.0, 23064014.0, "fli gal4 uas hlx endo 48h s1 R1.fastq.gz", "0:75 1:75", "A:658343595;C:1050309687;G:1097759573;T:650443491;N:2745754", 75, 75, null, null, 658343595, 1050309687, 1097759573, 650443491, 2745754, "SRX2902570", "SRS2269173", "SRA573518", "BRFAA|Molecular Biology", "BRFAA", 2, 0.57077, 0.57481, 0.2173, 0.2185, 0.79553, 0.79762, 0.50405, 0.48708, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Greece", "2017-06-13", "Undetermined", "Undetermined", "Heart", "Cardiovascular System"], [48625, "SRR7280652", "SRX4184230", "SRS3395609", "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", null, null, null, "Telencephalon", "Brain Telenc", null, "strain:AB|age:adult|sex:pooled male and female|tissue:Telencephalon|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: telencephalon", "Brain Telenc", "Brain Telenc", "RNA from dissociated telencephalons of males and females", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "Brain_Telenc_R1-125.fq.gz Brain_Telenc_R2-125.fq.gz", "fastq fastq", 71366993000.0, 285467972.0, "Brain Telenc R1 125.fq.gz", "0:125 1:125", "A:19965884492;C:15794543428;G:15865015134;T:19703234174;N:38315772", 125, 125, null, null, 19965884492, 15794543428, 15865015134, 19703234174, 38315772, "SRX4184230", "SRS3395609", "SRA717220", "Centre for Genomic Regulation|Systems Biology Department", "Centre for Genomic Regulation", 2, 0.94146, 0.94273, 0.14194, 0.14162, 0.70167, 0.70396, 0.52125, 0.51616, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2019-01-22", "Adult", "Adult", "Brain", "Nervous System"], [48626, "SRR7280653", "SRX4184229", "SRS3395610", "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", null, null, null, "Cerebellum", "Cerebellum", null, "strain:AB|age:adult|sex:pooled male and female|tissue:Cerebellum|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: cerebellum", "Cerebellum", "Cerebellum", "RNA from dissociated cerebellum from males and females", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "Cerebellum_R1-125.fq.gz Cerebellum_R2-125.fq.gz", "fastq fastq", 34135866750.0, 136543467.0, "Cerebellum R2 125.fq.gz", "0:125 1:125", "A:9659073468;C:7434102293;G:7478952142;T:9549216912;N:14521935", 125, 125, null, null, 9659073468, 7434102293, 7478952142, 9549216912, 14521935, "SRX4184229", "SRS3395610", "SRA717220", "Centre for Genomic Regulation|Systems Biology Department", "Centre for Genomic Regulation", 2, 0.93517, 0.93417, 0.16496, 0.16457, 0.73695, 0.73476, 0.47363, 0.48287, 125, 125, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Spain", "2019-01-22", "Adult", "Adult", "Brain", "Nervous System"], [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", null, null, "Pool of one hundred 2hpf embryos", "2hpf embryos", "Embr 2hpf", null, "strain:AB|dev stage:2hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: 2hpf embryos", "Embr 2hpf", "Embr 2hpf", "RNA extracted from a pool of one hundred embryos", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "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, null, null, 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", null, "Spain", "2019-01-22", "Cleavage", "Embryo", "Trunk", "Surface Structure"], [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", null, null, "Pool of one hundred 8hpf embryos", "8hpf embryos", "Embr 8hpf", null, "strain:AB|dev stage:8hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: 8hpf embryos", "Embr 8hpf", "Embr 8hpf", "RNA extracted from a pool of one hundred embryos", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "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, null, null, 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", null, "Spain", "2019-01-22", "Gastrula", "Embryo", "Trunk", "Surface Structure"], [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", null, null, "Pool of one hundred 12hpf embryos", "12hpf embryos", "Embr 12hpf", null, "strain:AB|dev stage:12hpf|sex:pooled male and female|tissue:whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio: 12hpf embryos", "Embr 12hpf", "Embr 12hpf", "RNA extracted from a pool of one hundred embryos", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP149913", null, null, "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, null, null, 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", null, "Spain", "2019-01-22", "Segmentation", "Embryo", "Trunk", "Surface Structure"], [49091, "SRR7666344", "SRX4527573", "SRS3645455", "SRP157045", "PRJNA485433", "Diurnal transcriptome of adult zebrafish eye", "PRJNA485433", "Other", "Circadian rhythms orchestrate organism physiology to rhythmic changes in the environment  with the daily day and night cycle being the most prominent cyclic change occurring. In this regard  retina being a light responsive organ shows its vital physiological processes to be regulated by the clock. Here we report the diurnal transcriptome of zebrafish retina at Zt4day and Zt16night. We found 39% and 31% of the known genes to be expressed in retina at Zt4 and Zt16 respectively Reference genome Zv9. Also  by applying stringent cutoff of 5FPKM we identified 123 transcripts to be expressed differentially between the two time points  which contains few novel transcripts. In future  this study will contribute to the understanding of organ and species specific regulation of circadian rhythms and will also provide novel genes involved in the circadian regulation of retina.", null, null, null, null, "ZT4", null, "strain:Assam wild type|age:>3 month|dev stage:adult|sex:pooled male and female|tissue:eye|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "diurnal trancriptome of retina", "ZT4 101nt", "ZT4 101nt", "total transcriptome with Truseq stranded library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP157045", null, null, "ZF_Eye_CT4_gt50_R1_P.fastq ZF_Eye_CT4_gt50_R2_P.fastq", "fastq fastq", 4550334348.0, 22527137.0, "ZF Eye CT4 gt50 R1 P.fastq", "0:101.00 1:101.00", "A:1196463938;C:1068045211;G:1064853438;T:1220233324;N:738437", 101, 101, null, null, 1196463938, 1068045211, 1064853438, 1220233324, 738437, "SRX4527573", "SRS3645455", "SRA756783", "CSIR Insitute of Genomics and Integrative Biology|Functional Genomics", "CSIR Insitute of Genomics and Integrative Biology", 2, 0.92663, 0.92909, 0.33125, 0.32333, 0.70197, 0.7013, 0.55991, 0.52684, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "India", "2018-12-27", "Adult", "Adult", "Eye", "Sensory System"], [49092, "SRR7666345", "SRX4527572", "SRS3645456", "SRP157045", "PRJNA485433", "Diurnal transcriptome of adult zebrafish eye", "PRJNA485433", "Other", "Circadian rhythms orchestrate organism physiology to rhythmic changes in the environment  with the daily day and night cycle being the most prominent cyclic change occurring. In this regard  retina being a light responsive organ shows its vital physiological processes to be regulated by the clock. Here we report the diurnal transcriptome of zebrafish retina at Zt4day and Zt16night. We found 39% and 31% of the known genes to be expressed in retina at Zt4 and Zt16 respectively Reference genome Zv9. Also  by applying stringent cutoff of 5FPKM we identified 123 transcripts to be expressed differentially between the two time points  which contains few novel transcripts. In future  this study will contribute to the understanding of organ and species specific regulation of circadian rhythms and will also provide novel genes involved in the circadian regulation of retina.", null, null, null, null, "ZT16", null, "strain:Assam wild type|age:>3months|dev stage:adult|sex:pooled male and female|tissue:eye|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "diurnal transcriptome of retina", "ZT16 101nt", "ZT16 101nt", "total transcriptome with Truseq stranded library", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP157045", null, null, "ZF_Eye_CT016_gt50_R1_P.fastq ZF_Eye_CT016_gt50_R2_P.fastq", "fastq fastq", 14656436974.0, 72560331.0, "ZF Eye CT016 gt50 R1 P.fastq", "0:100.99 1:100.99", "A:3573626926;C:3724443056;G:3714836422;T:3641178568;N:2352002", 100, 100, null, null, 3573626926, 3724443056, 3714836422, 3641178568, 2352002, "SRX4527572", "SRS3645456", "SRA756783", "CSIR Insitute of Genomics and Integrative Biology|Functional Genomics", "CSIR Insitute of Genomics and Integrative Biology", 2, 0.917, 0.91899, 0.27178, 0.261, 0.72135, 0.72082, 0.63885, 0.63571, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "India", "2018-08-10", "Adult", "Adult", "Eye", "Sensory System"], [49332, "SRR7888761", "SRX4726390", "SRS3810123", "SRP162319", "PRJNA492406", "Profiles analysis reveals circRNAs involving zebrafish physiological development", "GSE120289", "Transcriptome Analysis", "Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins  modulation of transcription and interference with splicing  and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development  further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period  gastrula period  segmentation period  throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes  then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways  cardiovascular system development  retinal ganglion cell axon guidance and so on. Moreover  circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b  miR 124 and so on  some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points  suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula  gastrula  segmentation  throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.", null, null, null, "72h", "GSM3397729", null, "source name:Embryo|tissue:Embryo|age:72 hpf|developmental stage:incubation|strain:Tubingenz|genotype:WT", "72h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters \"mem  T 19\". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs  raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC \u22652 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.", "Embryo", "Zebrafish were reared at 28\u00b11\u2103 in a water circulatory system that osmotic pressure stability  UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5\u00b10.5\u2103. Morphological features were used to judge the stage of embryonic development.", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer\u2019s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer\u2019s instructions Illumina", null, "tissue:Embryo|age:72 hpf|developmental stage:incubation|strain:Tubingenz|genotype:WT", "GSM3397729", "GSM3397729: 72h; Danio rerio; ncRNA Seq", "GSM3397729", null, "1", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina", "GEO Accession:GSM3397729", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162319", null, null, "72h_1.fq.gz 72h_2.fq.gz", "fastq fastq", 12097159200.0, 40323864.0, "GSM3397729 r1", "0:150 1:150", "A:2809307023;C:3169515166;G:3184429517;T:2931448896;N:2458598", 150, 150, null, null, 2809307023, 3169515166, 3184429517, 2931448896, 2458598, "SRX4726390", "SRS3810123", "SRA781248", "GEO", "Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital", 2, 0.90426, 0.90717, 0.27165, 0.26439, 0.70739, 0.72397, 0.60155, 0.60561, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-09-21", "Larval", "Larval", "Embryo Imprecise", "All anatomical structures"], [49333, "SRR7888760", "SRX4726389", "SRS3810122", "SRP162319", "PRJNA492406", "Profiles analysis reveals circRNAs involving zebrafish physiological development", "GSE120289", "Transcriptome Analysis", "Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins  modulation of transcription and interference with splicing  and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development  further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period  gastrula period  segmentation period  throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes  then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways  cardiovascular system development  retinal ganglion cell axon guidance and so on. Moreover  circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b  miR 124 and so on  some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points  suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula  gastrula  segmentation  throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.", null, null, null, "48h", "GSM3397728", null, "source name:Embryo|tissue:Embryo|age:48 hpf|developmental stage:throat|strain:Tubingenz|genotype:WT", "48h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters \"mem  T 19\". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs  raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC \u22652 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.", "Embryo", "Zebrafish were reared at 28\u00b11\u2103 in a water circulatory system that osmotic pressure stability  UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5\u00b10.5\u2103. Morphological features were used to judge the stage of embryonic development.", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer\u2019s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer\u2019s instructions Illumina", null, "tissue:Embryo|age:48 hpf|developmental stage:throat|strain:Tubingenz|genotype:WT", "GSM3397728", "GSM3397728: 48h; Danio rerio; ncRNA Seq", "GSM3397728", null, "1", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina", "GEO Accession:GSM3397728", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162319", null, null, "48h_2.fq.gz 48h_1.fq.gz", "fastq fastq", 13525174500.0, 45083915.0, "GSM3397728 r1", "0:150 1:150", "A:2352542664;C:4312268007;G:4256218842;T:2601416951;N:2728036", 150, 150, null, null, 2352542664, 4312268007, 4256218842, 2601416951, 2728036, "SRX4726389", "SRS3810122", "SRA781248", "GEO", "Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital", 2, 0.91614, 0.91412, 0.12891, 0.12218, 0.76751, 0.77948, 0.71008, 0.73648, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-09-21", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [49334, "SRR7888759", "SRX4726388", "SRS3810120", "SRP162319", "PRJNA492406", "Profiles analysis reveals circRNAs involving zebrafish physiological development", "GSE120289", "Transcriptome Analysis", "Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins  modulation of transcription and interference with splicing  and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development  further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period  gastrula period  segmentation period  throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes  then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways  cardiovascular system development  retinal ganglion cell axon guidance and so on. Moreover  circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b  miR 124 and so on  some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points  suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula  gastrula  segmentation  throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.", null, null, null, "24h", "GSM3397727", null, "source name:Embryo|tissue:Embryo|age:24 hpf|developmental stage:segmentation|strain:Tubingenz|genotype:WT", "24h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters \"mem  T 19\". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs  raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC \u22652 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.", "Embryo", "Zebrafish were reared at 28\u00b11\u2103 in a water circulatory system that osmotic pressure stability  UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5\u00b10.5\u2103. Morphological features were used to judge the stage of embryonic development.", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer\u2019s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer\u2019s instructions Illumina", null, "tissue:Embryo|age:24 hpf|developmental stage:segmentation|strain:Tubingenz|genotype:WT", "GSM3397727", "GSM3397727: 24h; Danio rerio; ncRNA Seq", "GSM3397727", null, "1", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina", "GEO Accession:GSM3397727", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162319", null, null, "24h_1.fq.gz 24h_2.fq.gz", "fastq fastq", 14333175000.0, 47777250.0, "GSM3397727 r1", "0:150 1:150", "A:2728754113;C:4276840070;G:4344116037;T:2980570245;N:2894535", 150, 150, null, null, 2728754113, 4276840070, 4344116037, 2980570245, 2894535, "SRX4726388", "SRS3810120", "SRA781248", "GEO", "Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital", 2, 0.89719, 0.89478, 0.18044, 0.18119, 0.76942, 0.7876, 0.75758, 0.75366, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-09-21", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [49335, "SRR7888758", "SRX4726387", "SRS3810121", "SRP162319", "PRJNA492406", "Profiles analysis reveals circRNAs involving zebrafish physiological development", "GSE120289", "Transcriptome Analysis", "Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins  modulation of transcription and interference with splicing  and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development  further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period  gastrula period  segmentation period  throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes  then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways  cardiovascular system development  retinal ganglion cell axon guidance and so on. Moreover  circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b  miR 124 and so on  some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points  suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula  gastrula  segmentation  throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.", null, null, null, "8h", "GSM3397726", null, "source name:Embryo|tissue:Embryo|age:8 hpf|developmental stage:gastrula|strain:Tubingenz|genotype:WT", "8h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters \"mem  T 19\". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs  raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC \u22652 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.", "Embryo", "Zebrafish were reared at 28\u00b11\u2103 in a water circulatory system that osmotic pressure stability  UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5\u00b10.5\u2103. Morphological features were used to judge the stage of embryonic development.", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer\u2019s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer\u2019s instructions Illumina", null, "tissue:Embryo|age:8 hpf|developmental stage:gastrula|strain:Tubingenz|genotype:WT", "GSM3397726", "GSM3397726: 8h; Danio rerio; ncRNA Seq", "GSM3397726", null, "1", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina", "GEO Accession:GSM3397726", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162319", null, null, "8h_2.fq.gz 8h_1.fq.gz", "fastq fastq", 15434085600.0, 51446952.0, "GSM3397726 r1", "0:150 1:150", "A:2318158791;C:5134519748;G:5292209580;T:2686084369;N:3113112", 150, 150, null, null, 2318158791, 5134519748, 5292209580, 2686084369, 3113112, "SRX4726387", "SRS3810121", "SRA781248", "GEO", "Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital", 2, 0.95788, 0.95584, 0.07233, 0.07686, 0.81889, 0.82946, 0.81383, 0.80143, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-09-21", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [49336, "SRR7888757", "SRX4726386", "SRS3810119", "SRP162319", "PRJNA492406", "Profiles analysis reveals circRNAs involving zebrafish physiological development", "GSE120289", "Transcriptome Analysis", "Recent studies have found that known functions of circRNAs include sequestration of microRNAs or proteins  modulation of transcription and interference with splicing  and even translation to produce poly peptides. The zebrafish model is also demonstrably similar to humans in many studies. In order to explore the changes in circRNAs during embryonic development  further to research the mechanism of action of circRNAs in development related diseases. Zebrafish embryos at blastula period  gastrula period  segmentation period  throat stage and incubation period were collected. Illumina deep sequencing technology and CIRI algorithm were used to detecting circRNAs. Totally we identified 1028 circRNAs junction reads = 5 and p < 0.05. Considering that circRNAs function is related to host genes  then bioinformatics analysis revealed these differentially expressed host genes are involved in NOTCH signaling pathways  cardiovascular system development  retinal ganglion cell axon guidance and so on. Moreover  circRNAs can participate in biological regulation through miRNA sponges function. TargetScan and miRanda were used to predict 73 miRNAs binding to circRNAs such as miR 19b  miR 124 and so on  some miRNAs play important roles in embryogenesis. The peak expression of circRNAs is distributed at different time points  suggesting that it may be involved in embryogenesis at different stages. Our study provides a foundation for understanding the dynamic regulation of circRNA transcriptomes during embryogenesis and identifies novel key circRNAs that might control embryonic development in zebrafish model. Overall design: circRNAs of five periods blastula  gastrula  segmentation  throat and incubation in zebrafish were detected by deep sequencing using Illumina HiSeq 2500.", null, null, null, "4.5h", "GSM3397725", null, "source name:Embryo|tissue:Embryo|age:4.5 hpf|developmental stage:blastula|strain:Tubingenz|genotype:WT", "4.5h", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to z10 whole genome using bwa 0.7.5a r405 with parameters \"mem  T 19\". CircRNA prediction of sequencing results by CIRI algorithm v1.1. SRPBM Spliced Reads per Billion Mapped Reads=number of circular reads/number of mapped reads units in billion/read length used to normalize the expression of circRNAs. For differential expression analysis of circRNAs  raw counts of reads that spanned a particular head to tail junction were analyzed using edgeR package version 3.12.1 with TMM normalization in generalized linear model. The Trimmed Mean of M values TMM normalization method was used to remove the size basis of sequencing libraries between samples. The following criteria were used to screen out significantly differentially expressed circRNAs: Fold change FC \u22652 and p< 0.05. Genome build: z10 Supplementary files format and content: tab delimited text files include SRPBM values and junction reads for each Sample.", "Embryo", "Zebrafish were reared at 28\u00b11\u2103 in a water circulatory system that osmotic pressure stability  UV disinfects and aerates the recycled water.The embryos were obtained post spontaneous mating from sexually mature wild type WT adult fish and cultivated at 28.5\u00b10.5\u2103. Morphological features were used to judge the stage of embryonic development.", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer\u2019s protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer\u2019s instructions Illumina", null, "tissue:Embryo|age:4.5 hpf|developmental stage:blastula|strain:Tubingenz|genotype:WT", "GSM3397725", "GSM3397725: 4.5h; Danio rerio; ncRNA Seq", "GSM3397725", null, "1", "Total RNA was isolated using the standard TRIzol Invitrogen protocol Genomic DNA was removed by DNase treatment. Then the total RNA were subject to ribosomal RNA depletion according to the manufacturer's protocol of RiboMinus kit Life Technology. The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bio analyzer. Strand specific libraries were constructed by following the manufacturer's instructions Illumina", "GEO Accession:GSM3397725", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP162319", null, null, "4_5h_2.fq.gz 4_5h_1.fq.gz", "fastq fastq", 12988242600.0, 43294142.0, "GSM3397725 r1", "0:150 1:150", "A:2232301074;C:3998769528;G:4233380689;T:2521224783;N:2566526", 150, 150, null, null, 2232301074, 3998769528, 4233380689, 2521224783, 2566526, "SRX4726386", "SRS3810119", "SRA781248", "GEO", "Department of Pediatrics, Nanjing Maternity and Child Health Care Hospital", 2, 0.96961, 0.96817, 0.05627, 0.05463, 0.77068, 0.78198, 0.74899, 0.75759, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2018-09-21", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [53507, "SRR9899207", "SRX6651058", "SRS5212730", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish bmpr2b mutant", null, "strain:AB zebrafish|isolate:mutant|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan  China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton  muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of mutant fish", "mutant1", "mutant1", "Total RNA was isolated from the 15 dpf dpf bmpr2b mutant larval fishes using RNAiso Plus Reagent TaKaRa  China according to the manufacturers protocol. post RNA quality and quantity control  the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "m1_1.fq.gz m1_2.fq.gz", "fastq fastq", 8332769700.0, 27775899.0, "m1 1.fq.gz", "0:150 1:150", "A:2157086519;C:2009631895;G:2036110721;T:2129846686;N:93879", 150, 150, null, null, 2157086519, 2009631895, 2036110721, 2129846686, 93879, "SRX6651058", "SRS5212730", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95476, 0.95486, 0.06414, 0.06413, 0.66115, 0.66156, 0.47619, 0.47307, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53508, "SRR9899208", "SRX6651057", "SRS5212731", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish wild", null, "strain:AB zebrafish|isolate:wild fish|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan  China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton  muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of wild fish", "wild3", "wild3", "Total RNA was isolated from the 15 dpf dpf wild larval fishes using RNAiso Plus Reagent TaKaRa  China according to the manufacturers protocol. post RNA quality and quantity control  the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "w3_1.fq.gz w3_2.fq.gz", "fastq fastq", 8715170100.0, 29050567.0, "w3 1.fq.gz", "0:150 1:150", "A:2265881414;C:2090871457;G:2123814411;T:2234503490;N:99328", 150, 150, null, null, 2265881414, 2090871457, 2123814411, 2234503490, 99328, "SRX6651057", "SRS5212731", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95085, 0.95146, 0.06684, 0.0667, 0.65886, 0.6588, 0.47356, 0.48005, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53509, "SRR9899209", "SRX6651056", "SRS5212731", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish wild", null, "strain:AB zebrafish|isolate:wild fish|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan  China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton  muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of wild fish", "wild2", "wild2", "Total RNA was isolated from the 15 dpf dpf wild larval fishes using RNAiso Plus Reagent TaKaRa  China according to the manufacturers protocol. post RNA quality and quantity control  the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "w2_1.fq.gz w2_2.fq.gz", "fastq fastq", 9346269600.0, 31154232.0, "w2 1.fq.gz", "0:150 1:150", "A:2421899244;C:2254190061;G:2283375277;T:2386698720;N:106298", 150, 150, null, null, 2421899244, 2254190061, 2283375277, 2386698720, 106298, "SRX6651056", "SRS5212731", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95445, 0.95603, 0.06361, 0.06276, 0.6616, 0.66121, 0.47635, 0.47716, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53510, "SRR9899210", "SRX6651055", "SRS5212731", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish wild", null, "strain:AB zebrafish|isolate:wild fish|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan  China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton  muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of wild fish", "wild1", "wild1", "Total RNA was isolated from the 15 dpf dpf wild larval fishes using RNAiso Plus Reagent TaKaRa  China according to the manufacturers protocol. post RNA quality and quantity control  the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "w1_1.fq.gz w1_2.fq.gz", "fastq fastq", 8756101500.0, 29187005.0, "w1 1.fq.gz", "0:150 1:150", "A:2274557262;C:2102935324;G:2133197715;T:2245310628;N:100571", 150, 150, null, null, 2274557262, 2102935324, 2133197715, 2245310628, 100571, "SRX6651055", "SRS5212731", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95161, 0.95225, 0.06682, 0.06678, 0.65831, 0.65993, 0.47144, 0.47166, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53511, "SRR9899211", "SRX6651054", "SRS5212730", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish bmpr2b mutant", null, "strain:AB zebrafish|isolate:mutant|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan  China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton  muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of mutant fish", "mutant3", "mutant3", "Total RNA was isolated from the 15 dpf dpf bmpr2b mutant larval fishes using RNAiso Plus Reagent TaKaRa  China according to the manufacturers protocol. post RNA quality and quantity control  the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "m3_1.fq.gz m3_2.fq.gz", "fastq fastq", 8385335400.0, 27951118.0, "m3 1.fq.gz", "0:150 1:150", "A:2179183324;C:2013493686;G:2044351918;T:2148211353;N:95119", 150, 150, null, null, 2179183324, 2013493686, 2044351918, 2148211353, 95119, "SRX6651054", "SRS5212730", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.94884, 0.94904, 0.0643, 0.06403, 0.66145, 0.66316, 0.46951, 0.4767, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [53512, "SRR9899212", "SRX6651053", "SRS5212730", "SRP217299", "PRJNA558506", "Bmpr2b mutant zebrafish sequencing", "PRJNA558506", "Other", "In order to explore the differential expression genes and related pathways caused by bmpr2b deletion in zebrafish. The comparative transcriptome analysis between wild and mutant samples was conducted.", null, null, null, null, "zebrafish bmpr2b mutant", null, "strain:AB zebrafish|isolate:mutant|breed:zebrafish|cultivar:zebrafish|ecotype:Wuhan  China|age:15 days|dev stage:larval fish|sex:unknown|tissue:skeleton  muscle|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of mutant fish", "mutant2", "mutant2", "Total RNA was isolated from the 15 dpf dpf bmpr2b mutant larval fishes using RNAiso Plus Reagent TaKaRa  China according to the manufacturers protocol. post RNA quality and quantity control  the transcriptome equencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina NEB  USA following manufacturers recommendations and index codes were added to attribute sequences to each sample.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP217299", null, null, "m2_1.fq.gz m2_2.fq.gz", "fastq fastq", 8728240500.0, 29094135.0, "m2 1.fq.gz", "0:150 1:150", "A:2262292258;C:2101600854;G:2129980194;T:2234266968;N:100226", 150, 150, null, null, 2262292258, 2101600854, 2129980194, 2234266968, 100226, "SRX6651053", "SRS5212730", "SRA932406", "Huazhong Agricultural University|College of Fisheries, Key Lab of Freshwater Animal", "Huazhong Agricultural University", 2, 0.95297, 0.95358, 0.06449, 0.06417, 0.65965, 0.65918, 0.47932, 0.4645, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2019-08-03", "Larval", "Larval", "Muscle", "Muscular System"], [55379, "SRR10323881", "SRX7034716", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2", "10", "10", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz", "fastq fastq", 3356658750.0, 22377725.0, "RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:875300673;C:782517555;G:796855605;T:901672776;N:312141", 75, 75, null, null, 875300673, 782517555, 796855605, 901672776, 312141, "SRX7034716", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.68437, 0.73326, 0.04743, 0.05194, 0.80241, 0.80517, 0.51875, 0.52196, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55380, "SRR10323882", "SRX7034715", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1", "9", "9", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz RNA_seq control for lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz", "fastq fastq", 3459242400.0, 23061616.0, "RNA seq control for lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:924400584;C:762078140;G:779330250;T:993109509;N:323917", 75, 75, null, null, 924400584, 762078140, 779330250, 993109509, 323917, "SRX7034715", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.67032, 0.73764, 0.07629, 0.08303, 0.80856, 0.80748, 0.52094, 0.52695, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55381, "SRR10323883", "SRX7034714", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2", "8", "8", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz", "fastq fastq", 3238312500.0, 21588750.0, "RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:881635390;C:656958401;G:673596788;T:1025824968;N:296953", 75, 75, null, null, 881635390, 656958401, 673596788, 1025824968, 296953, "SRX7034714", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.59623, 0.72377, 0.07781, 0.08944, 0.80608, 0.8016, 0.53277, 0.53095, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55382, "SRR10323884", "SRX7034713", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1", "7", "7", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 3255021150.0, 21700141.0, "RNA seq mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:858912760;C:733048670;G:750496371;T:912263495;N:299854", 75, 75, null, null, 858912760, 733048670, 750496371, 912263495, 299854, "SRX7034713", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.65481, 0.71883, 0.05477, 0.05995, 0.7903, 0.7921, 0.51367, 0.51188, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55383, "SRR10323885", "SRX7034712", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2", "6", "6", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq control for mda5 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz", "fastq fastq", 2413394850.0, 16089299.0, "RNA seq control for mda5 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:660807483;C:490677840;G:505039519;T:756646234;N:223774", 75, 75, null, null, 660807483, 490677840, 505039519, 756646234, 223774, "SRX7034712", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.60009, 0.72319, 0.09185, 0.10528, 0.82175, 0.81815, 0.5234, 0.51725, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55384, "SRR10323886", "SRX7034711", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. 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We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. 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We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. 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We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1", "23", "23", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 5656815000.0, 37712100.0, "RNA seq decitabine treatment in hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:1487198866;C:1332723090;G:1275197163;T:1514410765;N:47285116", 75, 75, null, null, 1487198866, 1332723090, 1275197163, 1514410765, 47285116, "SRX7034698", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.86399, 0.76012, 0.0587, 0.05779, 0.76461, 0.9105, 0.49754, 0.51037, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55388, "SRR10323900", "SRX7034697", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  VPA treatment in hemogenic endothelial cell 26hpf replicate 2", "22", "22", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz", "fastq fastq", 5978780250.0, 39858535.0, "RNA seq VPA treatment in hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:1580804547;C:1404640964;G:1399714637;T:1593586843;N:33259", 75, 75, null, null, 1580804547, 1404640964, 1399714637, 1593586843, 33259, "SRX7034697", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.92216, 0.92477, 0.04155, 0.04126, 0.74537, 0.7512, 0.48148, 0.49049, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55389, "SRR10323901", "SRX7034696", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. 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We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. 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Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2", "18", "18", "TruSeq stranded mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz", "fastq fastq", 4925792850.0, 32838619.0, "RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:1327496924;C:1143172265;G:1121827107;T:1332765205;N:531349", 75, 75, null, null, 1327496924, 1143172265, 1121827107, 1332765205, 531349, "SRX7034692", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.9235, 0.923, 0.07189, 0.07157, 0.74576, 0.7486, 0.46424, 0.46997, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55394, "SRR10323906", "SRX7034691", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1", "17", "17", "TruSeq stranded mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq mda5_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 4481194200.0, 29874628.0, "RNA seq mda5 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:1207561849;C:1040055195;G:1022613796;T:1210492037;N:471323", 75, 75, null, null, 1207561849, 1040055195, 1022613796, 1210492037, 471323, "SRX7034691", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.92094, 0.92157, 0.07292, 0.07281, 0.74704, 0.75067, 0.47205, 0.47416, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55395, "SRR10323907", "SRX7034690", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2", "16", "16", "TruSeq stranded mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz", "fastq fastq", 2071385250.0, 13809235.0, "RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:497024628;C:535934066;G:538798491;T:499539772;N:88293", 75, 75, null, null, 497024628, 535934066, 538798491, 499539772, 88293, "SRX7034690", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.92507, 0.92563, 0.0745, 0.07106, 0.74148, 0.74186, 0.5137, 0.52923, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55396, "SRR10323908", "SRX7034689", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1", "15", "15", "TruSeq stranded mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq rig_1_lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 1708336800.0, 11388912.0, "RNA seq rig 1 lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:413739883;C:438115098;G:440441368;T:415968029;N:72422", 75, 75, null, null, 413739883, 438115098, 440441368, 415968029, 72422, "SRX7034689", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.92948, 0.93123, 0.08112, 0.07757, 0.7472, 0.74921, 0.49384, 0.502, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55397, "SRR10323909", "SRX7034688", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 2", "14", "14", "TruSeq stranded mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz", "fastq fastq", 2742841800.0, 18285612.0, "RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:771268784;C:600759252;G:605972112;T:764554978;N:286674", 75, 75, null, null, 771268784, 600759252, 605972112, 764554978, 286674, "SRX7034688", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.91195, 0.91276, 0.15552, 0.15531, 0.7191, 0.7247, 0.487, 0.47379, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55398, "SRR10323910", "SRX7034687", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 1", "13", "13", "TruSeq stranded mRNA", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for double morphants endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 1909021350.0, 12726809.0, "RNA seq control for double morphants endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:536542827;C:420010389;G:423642042;T:528630203;N:195889", 75, 75, null, null, 536542827, 420010389, 423642042, 528630203, 195889, "SRX7034687", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.91535, 0.91534, 0.11578, 0.11457, 0.73705, 0.74373, 0.47609, 0.47115, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55399, "SRR10323911", "SRX7034686", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2", "12", "12", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz", "fastq fastq", 5135290500.0, 34235270.0, "RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:1339180940;C:1202946694;G:1230552771;T:1362120185;N:489910", 75, 75, null, null, 1339180940, 1202946694, 1230552771, 1362120185, 489910, "SRX7034686", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.66031, 0.70687, 0.04575, 0.04896, 0.81075, 0.81195, 0.50951, 0.47552, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55400, "SRR10323912", "SRX7034685", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq  lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1", "11", "11", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq lgp2 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 3890046300.0, 25933642.0, "RNA seq lgp2 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:1020376762;C:903218301;G:916043426;T:1050047618;N:360193", 75, 75, null, null, 1020376762, 903218301, 916043426, 1050047618, 360193, "SRX7034685", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.70733, 0.75223, 0.05929, 0.06271, 0.80807, 0.81071, 0.48475, 0.49323, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55401, "SRR10323913", "SRX7034684", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2", "2", "2", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R1.fastq.gz RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 2_R2.fastq.gz", "fastq fastq", 2547796350.0, 16985309.0, "RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 2 R1.fastq.gz", "0:75 1:75", "A:686259539;C:560800822;G:567842650;T:732652800;N:240539", 75, 75, null, null, 686259539, 560800822, 567842650, 732652800, 240539, "SRX7034684", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.70188, 0.75886, 0.08072, 0.08833, 0.8034, 0.80649, 0.51507, 0.5194, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [55402, "SRR10323914", "SRX7034683", "SRS5554730", "SRP226614", "PRJNA578896", "Repetitive elements engage Rig I and Mda5 in interplay with Lgp2 to enhance hematopoietic stem cell emergence", "PRJNA578896", "Other", "In this study we examine the role of RIG I like receptors RLRs in hematopoietic stem and progenitor cell formation. We have performed extensive expression analysis and chromatin accessibility assays on endothelial and hemogenic endothelial cells in knockdown animals for all the RLR receptors. Additionally we did expression analysis on animals with knockdown of two receptors. Finally we examined the upregulation of repetitive elements in hemogenic endothelial cells post treatment with valproic acid VPA or decitabine.", null, null, null, null, "danRer10 raw data", null, "strain:AB/tu|age:not applicable|sex:pooled male and female|tissue:endothelial and hemogenic endothelial|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1", "1", "1", "NEBNext Low Input RNA Library Prep Kit", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 3000", null, "SRP226614", null, null, "RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R1.fastq.gz RNA_seq control for rig_1 morpholino injected endothelial_hemogenic endothelial cell 26hpf replicate 1_R2.fastq.gz", "fastq fastq", 2438070600.0, 16253804.0, "RNA seq control for rig 1 morpholino injected endothelial hemogenic endothelial cell 26hpf replicate 1 R1.fastq.gz", "0:75 1:75", "A:654282012;C:534555119;G:543878428;T:705130425;N:224616", 75, 75, null, null, 654282012, 534555119, 543878428, 705130425, 224616, "SRX7034683", "SRS5554730", "SRA983011", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany|Department of Cellular and Molecular Immunology", "Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany", 2, 0.69336, 0.75626, 0.09168, 0.09896, 0.80166, 0.80253, 0.51795, 0.52538, 75, 75, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "Germany", "2019-10-24", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [67823, "SRR17335719", "SRX13511115", "SRS11405356", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CPF3", "GSM5754470", null, "source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing", "CPF3", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CPF toxication", "GSM5754470", "GSM5754470: CPF3; Danio rerio; ncRNA Seq", "GSM5754470 r1", "GSM5754470", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CPF3_1.fq.gz CPF3_2.fq.gz", "fastq fastq", 12726241500.0, 42420805.0, "GSM5754470 r1", "0:150 1:150", "A:3447613023;C:2896153797;G:2922038320;T:3459698412;N:737948", 150, 150, null, null, 3447613023, 2896153797, 2922038320, 3459698412, 737948, "SRX13511115", "SRS11405356", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.89399, 0.89612, 0.38172, 0.37657, 0.66628, 0.66799, 0.53056, 0.53213, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67824, "SRR17335720", "SRX13511114", "SRS11405355", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CPF2", "GSM5754469", null, "source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing", "CPF2", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CPF toxication", "GSM5754469", "GSM5754469: CPF2; Danio rerio; ncRNA Seq", "GSM5754469 r1", "GSM5754469", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CPF2_1.fq.gz CPF2_2.fq.gz", "fastq fastq", 14881715100.0, 49605717.0, "GSM5754469 r1", "0:150 1:150", "A:4214905088;C:3201163283;G:3225795074;T:4239665352;N:186303", 150, 150, null, null, 4214905088, 3201163283, 3225795074, 4239665352, 186303, "SRX13511114", "SRS11405355", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.87491, 0.87638, 0.40844, 0.40479, 0.67123, 0.67018, 0.49174, 0.48952, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67825, "SRR17335721", "SRX13511113", "SRS11405354", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CPF1", "GSM5754468", null, "source name:Brain tissue|tissue:Brain|treatment:CPF toxication|geo loc name:missing|collection date:missing", "CPF1", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CPF toxication", "GSM5754468", "GSM5754468: CPF1; Danio rerio; ncRNA Seq", "GSM5754468 r1", "GSM5754468", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CPF1_1.fq.gz CPF1_2.fq.gz", "fastq fastq", 16447798800.0, 54825996.0, "GSM5754468 r1", "0:150 1:150", "A:4454573413;C:3748270411;G:3776995203;T:4467442717;N:517056", 150, 150, null, null, 4454573413, 3748270411, 3776995203, 4467442717, 517056, "SRX13511113", "SRS11405354", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.89313, 0.8947, 0.35381, 0.35194, 0.64954, 0.64831, 0.51962, 0.52475, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67826, "SRR17335722", "SRX13511112", "SRS11405353", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CYP3", "GSM5754467", null, "source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing", "CYP3", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CYP toxication", "GSM5754467", "GSM5754467: CYP3; Danio rerio; ncRNA Seq", "GSM5754467 r1", "GSM5754467", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CYP3_1.fq.gz CYP3_2.fq.gz", "fastq fastq", 13417868100.0, 44726227.0, "GSM5754467 r1", "0:150 1:150", "A:3645134270;C:3041754103;G:3084809543;T:3645750889;N:419295", 150, 150, null, null, 3645134270, 3041754103, 3084809543, 3645750889, 419295, "SRX13511112", "SRS11405353", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.86122, 0.8638, 0.4112, 0.40785, 0.68738, 0.68519, 0.54768, 0.44856, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67827, "SRR17335723", "SRX13511111", "SRS11405352", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CYP2", "GSM5754466", null, "source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing", "CYP2", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CYP toxication", "GSM5754466", "GSM5754466: CYP2; Danio rerio; ncRNA Seq", "GSM5754466 r1", "GSM5754466", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CYP2_1.fq.gz CYP2_2.fq.gz", "fastq fastq", 13096007700.0, 43653359.0, "GSM5754466 r1", "0:150 1:150", "A:3638241155;C:2892284693;G:2925857490;T:3639296449;N:327913", 150, 150, null, null, 3638241155, 2892284693, 2925857490, 3639296449, 327913, "SRX13511111", "SRS11405352", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.85953, 0.86247, 0.41975, 0.41734, 0.68174, 0.67862, 0.52504, 0.5324, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67828, "SRR17335724", "SRX13511110", "SRS11405351", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "CYP1", "GSM5754465", null, "source name:Brain tissue|tissue:Brain|treatment:CYP toxication|geo loc name:missing|collection date:missing", "CYP1", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:CYP toxication", "GSM5754465", "GSM5754465: CYP1; Danio rerio; ncRNA Seq", "GSM5754465 r1", "GSM5754465", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "CYP1_1.fq.gz CYP1_2.fq.gz", "fastq fastq", 16372872000.0, 54576240.0, "GSM5754465 r1", "0:150 1:150", "A:4747286217;C:3417115980;G:3453793026;T:4754530080;N:146697", 150, 150, null, null, 4747286217, 3417115980, 3453793026, 4754530080, 146697, "SRX13511110", "SRS11405351", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.85322, 0.85414, 0.46298, 0.45901, 0.68016, 0.67866, 0.47694, 0.47897, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67829, "SRR17335725", "SRX13511109", "SRS11405350", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "Cont3", "GSM5754464", null, "source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing", "Cont3", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:No toxication", "GSM5754464", "GSM5754464: Cont3; Danio rerio; ncRNA Seq", "GSM5754464 r1", "GSM5754464", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "Cont3_1.fq.gz Cont3_2.fq.gz", "fastq fastq", 15202443900.0, 50674813.0, "GSM5754464 r1", "0:150 1:150", "A:4400470018;C:3173803928;G:3218623722;T:4409335756;N:210476", 150, 150, null, null, 4400470018, 3173803928, 3218623722, 4409335756, 210476, "SRX13511109", "SRS11405350", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.86129, 0.84677, 0.45657, 0.44799, 0.67884, 0.68083, 0.48291, 0.4763, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67830, "SRR17335726", "SRX13511108", "SRS11405349", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "Cont2", "GSM5754463", null, "source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing", "Cont2", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:No toxication", "GSM5754463", "GSM5754463: Cont2; Danio rerio; ncRNA Seq", "GSM5754463 r1", "GSM5754463", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "Cont2_1.fq.gz Cont2_2.fq.gz", "fastq fastq", 12927267600.0, 43090892.0, "GSM5754463 r1", "0:150 1:150", "A:3474574877;C:2959326086;G:3006553706;T:3486600752;N:212179", 150, 150, null, null, 3474574877, 2959326086, 3006553706, 3486600752, 212179, "SRX13511108", "SRS11405349", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.87695, 0.87907, 0.41673, 0.41416, 0.69266, 0.69266, 0.53339, 0.58145, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [67831, "SRR17335727", "SRX13511107", "SRS11405348", "SRP352585", "PRJNA792582", "circRNA based biomarker candidates for acute cypermethrin and chlorpyrisfos toxication in the brain of Zebrafish Danio rerio", "GSE192669", "Transcriptome Analysis", "Cypermethrin CYP and chlorpyrifos CPF are pesticides which are frequently used in agricultural areas around the world. These chemicals have been shown to cause serious toxicological damage in the brain of fish  which is non target organisms. However  circRNAs associated with acute brain toxicity caused by cypermethrin and chlorpyrifos have not been studied yet. In this study  circRNAs were identified and characterized using RNA seq in Zebrafish brains exposed to acute cypermethrin and chlorpyrifos toxicity. A total of 10375 circRNAs were detected. It was determined that 6 circRNAs were up regulated  10 circRNAs were down regulated in CYP brain samples compared to controls . In addition  it was found that 57 circRNAs are up regulated and 3 circRNAs down regulated in CPF brain samples compared to controls. Moreover  62 circRNAs were down regulated in the CYP samples  when CYP and CPF samples were compared. However  up regulated circRNA could not be detected. It was revealed that the detected circRNAs specifically regulated the MAPK signaling pathway  endocytosis mechanism  apoptosis and p53 signaling pathway. This study  which was conducted for the first time in terms of the subject of the study  could bring a different perspective especially to pesticide toxicity studies. Overall design: Examination of  circRNA related to acute cypermethrin and chlopyrifos toxication in brain of zebrafish", null, "pubmed:35304207", null, "Cont1", "GSM5754462", null, "source name:Brain tissue|tissue:Brain|treatment:No toxication|geo loc name:missing|collection date:missing", "Cont1", "Raw data raw reads of FASTQ format were firstly processed through in house scripts. In this step  clean data clean reads were obtained by removing reads containing adapter and poly N sequences and reads with low quality from raw data. At the same time  Q20  Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.An upgraded computational pipeline CIRCexplorer2 is applied to detect circRNAs and identify alternative back splicing in back spliced circular RNAs circRNAs The expression of circRNAs is usually represented by the fragments that are mapped to the back spliced exon\u2013exon junction sites. In addition to the raw fragment numbers  normalized RNA seq fragments that are mapped to a specific back spliced exon\u2013exon junction by total mapped fragments is used to quantitate circRNA expression. With FPM Fragments mapped to back  spliced junction Per Million mapped fragments  circRNAs from different samples with distinct sequencing depths can be directly compared. The input data for differential gene expression analysis is read counts from gene expression level analysis. For DESeq2 with biological replicates Differential expression analysis between two conditions/groups three biological replicates per condition was performed using DESeq2 R package. DESeq2 provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg\u2019s approach for controlling the False Discovery Rate FDR. Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed. A common way for searching shared functions among genes is to incorporate the biological knowledge provided by biological ontologies. Gene Ontology GO annotates genes to  biological processes  molecular functions  and cellular components in a directed acyclic graph structure  and Kyoto Encyclopedia of Genes and Genomes KEGG annotates genes to  pathways. KEGG is a database resource for understanding high level functions and utilities of the biological system  such as the cell  the organism and the ecosystem  from molecular level  information  especially large  scale molecular datasets generated by genome sequencing and other high  throughput experimental technologies http://www.genome.jp/kegg/. We  used KOBAS software to test the statistical enrichment of differential expression genes or circRNA host genes in KEGG pathways. circRNAs can act as miRNA sponge to inhibit the functioning of miRNAs. To further study the functions of circRNAs  microRNA target site in exons of circRNA loci were identified using miRanda animal species or psRobot plant species. software could be used to construct the circRNA miRNA gene networks. Genome build: UMD3.1", "Brain tissue", null, "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "tissue:Brain|treatment:No toxication", "GSM5754462", "GSM5754462: Cont1; Danio rerio; ncRNA Seq", "GSM5754462 r1", "GSM5754462", "1", "Total RNA was isolated with Trizol from brain tissues RNA libraries were prepared for sequencing using standard Illumina protocols", null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP352585", null, "loader:fastq load.py", "Cont1_1.fq.gz Cont1_2.fq.gz", "fastq fastq", 18395362500.0, 61317875.0, "GSM5754462 r1", "0:150 1:150", "A:5379624768;C:3792463355;G:3842313235;T:5380702187;N:258955", 150, 150, null, null, 5379624768, 3792463355, 3842313235, 5380702187, 258955, "SRX13511107", "SRS11405348", "SRA1349262", "Atat\u00fcrk University", "Atat\u00fcrk University", 2, 0.83439, 0.83446, 0.45703, 0.44894, 0.68828, 0.68578, 0.4957, 0.49639, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Turkey", "2021-12-27", "Undetermined", "Undetermined", "Brain", "Nervous System"], [75414, "SRR24517729", "SRX20302027", "SRS17627883", "SRP437283", "PRJNA971676", "zebrafish kiss genes knockouts deep sequencing", "PRJNA971676", "Other", "Mammals possess only one Kisspeptin gene  but in teleost like zebrafish  there are two copies. While knockout of Kiss1 results in infertility in mammals  knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.", null, null, null, "RNA seq of zebrafish:5dpf larvae kiss1kiss2DKO Replicate2", "zebrafish AO149 01T0008", null, "strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:kiss1 and kiss2 double knockout|geo loc name:China: Suzhou|sample type:whole organism|Replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish: larvae", "RNA Seq for zebrafish kiss1kiss2DKO larvae 2", "RNA Seq for zebrafish kiss1kiss2DKO larvae 2", "RNA Seq   zebrafish kiss1kiss2DKO larvae 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP437283", null, null, "Unknown_AO149-01T0008_good_1.fq.gz Unknown_AO149-01T0008_good_2.fq.gz", "fastq fastq", 6912158300.0, 23173882.0, "Unknown AO149 01T0008 good 1.fq.gz", "0:149.14 1:149.14", "A:1796529490;C:1649628994;G:1669079817;T:1796880198;N:39801", 149, 149, null, null, 1796529490, 1649628994, 1669079817, 1796880198, 39801, "SRX20302027", "SRS17627883", "SRA1636880", "Soochow University|Medical College", "Soochow University", 2, 0.95632, 0.95592, 0.06085, 0.06019, 0.66515, 0.66563, 0.47686, 0.47575, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-05-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [75415, "SRR24517730", "SRX20302026", "SRS17627882", "SRP437283", "PRJNA971676", "zebrafish kiss genes knockouts deep sequencing", "PRJNA971676", "Other", "Mammals possess only one Kisspeptin gene  but in teleost like zebrafish  there are two copies. While knockout of Kiss1 results in infertility in mammals  knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.", null, null, null, "RNA seq of zebrafish:5dpf larvae kiss1kiss2DKO Replicate1", "zebrafish AO149 01T0007", null, "strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:kiss1 and kiss2 double knockout|geo loc name:China: Suzhou|sample type:whole organism|Replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish: larvae", "RNA Seq for zebrafish kiss1kiss2DKO larvae 1", "RNA Seq  for zebrafish kiss1kiss2DKO larvae 1", "RNA Seq   zebrafish kiss1kiss2DKO larvae 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP437283", null, null, "Unknown_AO149-01T0007_good_1.fq.gz Unknown_AO149-01T0007_good_2.fq.gz", "fastq fastq", 8005311792.0, 26909041.0, "Unknown AO149 01T0007 good 1.fq.gz", "0:148.75 1:148.75", "A:2077441584;C:1913582326;G:1934120275;T:2080121870;N:45737", 148, 148, null, null, 2077441584, 1913582326, 1934120275, 2080121870, 45737, "SRX20302026", "SRS17627882", "SRA1636880", "Soochow University|Medical College", "Soochow University", 2, 0.9522, 0.95194, 0.06345, 0.06296, 0.65691, 0.65744, 0.48074, 0.48185, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-05-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [75416, "SRR24517731", "SRX20302025", "SRS17627881", "SRP437283", "PRJNA971676", "zebrafish kiss genes knockouts deep sequencing", "PRJNA971676", "Other", "Mammals possess only one Kisspeptin gene  but in teleost like zebrafish  there are two copies. While knockout of Kiss1 results in infertility in mammals  knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.", null, null, null, "RNA seq of zebrafish:5dpf larvae kiss2KO Replicate2", "zebrafish AO149 01T0006", null, "strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:kiss2 knockout|geo loc name:China: Suzhou|sample type:whole organism|Replicate:2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish: larvae", "RNA Seq for zebrafish kiss2KO larvae 2", "RNA Seq for zebrafish kiss2KO  larvae 2", "RNA Seq  zebrafish kiss2KO  larvae 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP437283", null, null, "Unknown_AO149-01T0006_good_1.fq.gz Unknown_AO149-01T0006_good_2.fq.gz", "fastq fastq", 7638089446.0, 25894588.0, "Unknown AO149 01T0006 good 1.fq.gz", "0:147.48 1:147.48", "A:2051138070;C:1759130157;G:1773591862;T:2054190526;N:38831", 147, 147, null, null, 2051138070, 1759130157, 1773591862, 2054190526, 38831, "SRX20302025", "SRS17627881", "SRA1636880", "Soochow University|Medical College", "Soochow University", 2, 0.94967, 0.94887, 0.08556, 0.08576, 0.64898, 0.64954, 0.47984, 0.48067, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-05-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [75417, "SRR24517732", "SRX20302024", "SRS17627879", "SRP437283", "PRJNA971676", "zebrafish kiss genes knockouts deep sequencing", "PRJNA971676", "Other", "Mammals possess only one Kisspeptin gene  but in teleost like zebrafish  there are two copies. While knockout of Kiss1 results in infertility in mammals  knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. Deep sequencing results will reveal the different downstream pathways affected by the two kiss genes and will help to understand their functions and functional divergence.", null, null, null, "RNA seq of zebrafish:5dpf larvae kiss2KO Replicate1", "zebrafish AO149 01T0005", null, "strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:kiss2 knockout|geo loc name:China: Suzhou|sample type:whole organism|Replicate:1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of zebrafish: larvae", "RNA Seq for zebrafish kiss2KO larvae 1", "RNA Seq for  zebrafish  kiss2KO  larvae 1", "RNA Seq   zebrafish  kiss2KO  larvae 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP437283", null, null, "Unknown_AO149-01T0005_good_1.fq.gz Unknown_AO149-01T0005_good_2.fq.gz", "fastq fastq", 7054134954.0, 23687508.0, "Unknown AO149 01T0005 good 1.fq.gz", "0:148.90 1:148.90", "A:1848389593;C:1667928954;G:1687707295;T:1850068763;N:40349", 148, 148, null, null, 1848389593, 1667928954, 1687707295, 1850068763, 40349, "SRX20302024", "SRS17627879", "SRA1636880", "Soochow University|Medical College", "Soochow University", 2, 0.94976, 0.95007, 0.07472, 0.07458, 0.65299, 0.65324, 0.48045, 0.47909, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-05-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [75418, "SRR24517733", "SRX20302023", "SRS17627880", "SRP437283", "PRJNA971676", "zebrafish kiss genes knockouts deep sequencing", "PRJNA971676", "Other", "Mammals possess only one Kisspeptin gene  but in teleost like zebrafish  there are two copies. While knockout of Kiss1 results in infertility in mammals  knockout of both kiss1 and kiss2 barely affects zebrafish reproduction. The functions and their functional divergence of zebrafish kiss genes are still not fully elucidated. 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