{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"size fractionation\", experiment.library_strategy = \"RNA-Seq\" and tissue_curation_coarse = \"All anatomical structures\"", "rows": [[15081, "ERR12476478", "ERX11852299", "ERS17743543", "ERP156655", "PRJEB71869", "Effects of paternal starvation in the offspring development of zebrafish", "33b9d14c-4211-4249-aede-f0f021d197e6", "Other", "Dietary restriction in the form of fasting is a putative key to a healthier and longer life  but these benefits may come at a trade off with reproductive fitness and may affect the following generations. The potential inter  and transgenerational effects of long term fasting and starvation are particularly poorly understood in vertebrates when they originate from the paternal line. We utilised the externally fertilising zebrafish amenable to a split egg clutch design to explore the male specific effects of fasting/starvation on fertility and fitness of offspring independently of maternal contribution. Eighteen days of fasting resulted in reduced fertility in exposed males. While average offspring survival was not affected  we detected increased larval growth rate in F1 offspring from starved males and more malformed embryos at 24 hpf in F2 offspring produced by F1 offspring from starved males. Comparing the transcriptomes of F1 embryos sired by starved and fed fathers revealed robust and reproducible increased expression of muscle composition genes but lower expression of lipid metabolism and lysosome genes in embryos from starved fathers. A large proportion of these genes showed enrichment in the yolk syncytial layer suggesting gene regulatory responses associated with metabolism of nutrients through paternal effects on extra embryonic tissues which are loaded with maternal factors. We compared the embryo transcriptomes to published adult transcriptome datasets and found comparable repressive effects of starvation on metabolism associated genes. These similarities suggest a physiologically relevant  directed and potentially adaptive response transmitted by the father  independently from the offspring's nutritional state  which was defined by the mother.", "ENA FIRST PUBLIC:2024 01 15|ENA LAST UPDATE:2024 01 15", null, "24 hpf embryo collected at 1242 from a cross with a starved father", "1242D Starved", "1242SD", null, "organism:Danio rerio|collection date:2018 02 02|scientific name:Danio rerio|common name:zebrafish|geographic location country and/or sea:Sweden", null, null, null, null, null, null, null, null, "NextSeq 500 sequencing", "ena EXPERIMENT TAB 15 01 2024 21:42:36:201 277053", "1242SD", "1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 500", null, "ERP156655", "NextSeq 500 sequencing", "ENA FIRST PUBLIC:2024 01 22|ENA LAST UPDATE:2024 01 22", "1242SD_S14_L003_R1_001.fastq.gz", "fastq", 95457398.0, 1268859.0, "ena RUN TAB 15 01 2024 21:42:36:202 277054", "0:75.23", "A:33339157;C:18598733;G:20350072;T:23148005;N:21431", 75, null, null, null, 33339157, 18598733, 20350072, 23148005, 21431, "ERX11852299", "ERS17743543", "ERA27788968", "University of Birmingham|European Nucleotide Archive", "University of Birmingham", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2024-01-15", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [28490, "SRR26319601", "SRX22027740", "SRS19100857", "SRP465070", "PRJNA1025141", "Danio rerio Raw sequence reads", "PRJNA1025141", "Other", "Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.", null, null, "Treatment", "CX3 for transcriptome 3", "CX3", null, "strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.67 E|treatment:Treatment Group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "ALST3 for transcriptome 3", "CX3 for transcriptome 3", "CX3 for transcriptome 3", "CX3 for transcriptome 3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP465070", null, null, "Unknown_AY803-03T0006_good_1.fq.gz Unknown_AY803-03T0006_good_2.fq.gz", "fastq fastq", 6255596356.0, 20929531.0, "Unknown AY803 03T0006 good 1.fq.gz", "0:149.44 1:149.44", "A:1657365560;C:1463722268;G:1467057724;T:1667269298;N:181506", 149, 149, null, null, 1657365560, 1463722268, 1467057724, 1667269298, 181506, "SRX22027740", "SRS19100857", "SRA1727563", "Soochow University|School of biology &amp; 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basic medical sciences", "Soochow University", 2, 0.88949, 0.92148, 0.08893, 0.0947, 0.65596, 0.65228, 0.46045, 0.47087, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28492, "SRR26319603", "SRX22027738", "SRS19100853", "SRP465070", "PRJNA1025141", "Danio rerio Raw sequence reads", "PRJNA1025141", "Other", "Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.", null, null, "Treatment", "CX1 for transcriptome 1", "CX1", null, "strain:AB|cultivar:WT|ecotype:China: Jiangsu|age:7 dpf|dev stage:Larvae|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.65 E|treatment:Treatment Group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "ALST1 for transcriptome 1", "CX1 for transcriptome 1", "CX1 for transcriptome 1", "CX1 for transcriptome 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP465070", null, null, "Unknown_AY803-03T0004_good_1.fq.gz Unknown_AY803-03T0004_good_2.fq.gz", "fastq fastq", 6478923586.0, 21662443.0, "Unknown AY803 03T0004 good 1.fq.gz", "0:149.54 1:149.54", "A:1712718473;C:1518937459;G:1523570227;T:1723510437;N:186990", 149, 149, null, null, 1712718473, 1518937459, 1523570227, 1723510437, 186990, "SRX22027738", "SRS19100853", "SRA1727563", "Soochow University|School of biology &amp; basic medical sciences", "Soochow University", 2, 0.89423, 0.9176, 0.08944, 0.09254, 0.6575, 0.65458, 0.4693, 0.46842, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28493, "SRR26319604", "SRX22027737", "SRS19100856", "SRP465070", "PRJNA1025141", "Danio rerio Raw sequence reads", "PRJNA1025141", "Other", "Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.", null, null, "Control", "con3 for transcriptome 3", "con3", null, "strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.64 E|treatment:Control Group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "con3 for transcriptome 3", "con3 for transcriptome 3", "con3 for transcriptome 3", "con3 for transcriptome 3", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP465070", null, null, "Unknown_AY803-03T0003_good_2.fq.gz Unknown_AY803-03T0003_good_1.fq.gz", "fastq fastq", 6341537566.0, 21218597.0, "Unknown AY803 03T0003 good 1.fq.gz", "0:149.43 1:149.43", "A:1679811754;C:1483631833;G:1489430825;T:1688482904;N:180250", 149, 149, null, null, 1679811754, 1483631833, 1489430825, 1688482904, 180250, "SRX22027737", "SRS19100856", "SRA1727563", "Soochow University|School of biology &amp; basic medical sciences", "Soochow University", 2, 0.88245, 0.91856, 0.09069, 0.09654, 0.66253, 0.65817, 0.46245, 0.46336, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28494, "SRR26319605", "SRX22027736", "SRS19100855", "SRP465070", "PRJNA1025141", "Danio rerio Raw sequence reads", "PRJNA1025141", "Other", "Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.", null, null, "Control", "con2 for transcriptome 2", "con2", null, "strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.63 E|treatment:Control Group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "con2 for transcriptome 2", "con2 for transcriptome 2", "con2 for transcriptome 2", "con2 for transcriptome 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP465070", null, null, "Unknown_AY803-03T0002_good_2.fq.gz Unknown_AY803-03T0002_good_1.fq.gz", "fastq fastq", 5709771178.0, 19100144.0, "Unknown AY803 03T0002 good 1.fq.gz", "0:149.47 1:149.47", "A:1505730979;C:1342843084;G:1346105868;T:1514941964;N:149283", 149, 149, null, null, 1505730979, 1342843084, 1346105868, 1514941964, 149283, "SRX22027736", "SRS19100855", "SRA1727563", "Soochow University|School of biology &amp; basic medical sciences", "Soochow University", 2, 0.8924, 0.91903, 0.09155, 0.09604, 0.65902, 0.65593, 0.4634, 0.46028, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [28495, "SRR26319606", "SRX22027735", "SRS19100852", "SRP465070", "PRJNA1025141", "Danio rerio Raw sequence reads", "PRJNA1025141", "Other", "Transcriptome sequencing of A. sinensis leaf tea treated on zebrafish sleep.", null, null, "Control", "con1 for transcriptome 1", "con1", null, "strain:AB|cultivar:Wild type|ecotype:China: Jiangsu suzhou|age:7 dpf|dev stage:Larvae phase|collection date:2022 11|geo loc name:China: Jiangsu suzhou|sex:pooled male and female|tissue:larvae|lat lon:31.32 N 120.62 E|treatment:Control Group|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "con1 for transcriptome 1", "con1 for transcriptome 1", "con1 for transcriptome 1", "con1 for transcriptome 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Ten", null, "SRP465070", null, null, "Unknown_AY803-03T0001_good_1.fq.gz Unknown_AY803-03T0001_good_2.fq.gz", "fastq fastq", 6544586118.0, 21872265.0, "Unknown AY803 03T0001 good 1.fq.gz", "0:149.61 1:149.61", "A:1731179229;C:1528367346;G:1541103688;T:1743735521;N:200334", 149, 149, null, null, 1731179229, 1528367346, 1541103688, 1743735521, 200334, "SRX22027735", "SRS19100852", "SRA1727563", "Soochow University|School of biology &amp; basic medical sciences", "Soochow University", 2, 0.87588, 0.92739, 0.08683, 0.09494, 0.65711, 0.6504, 0.46774, 0.47072, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2023-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [36195, "SRR042434", "SRX020028", "SRS066219", "SRP002411", "PRJNA126003", "A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity", "GSE21503", "Transcriptome Analysis", "Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs  we sequenced  small RNAs in wild type  maternal zygotic dicer MZdicer and MZago2 mutants  using zebrafish as a model system. We find that  in contrast to other miRNAs  miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs  followed by uridylation and trimming  generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type  MZago2  MZdicer at 48 hpf", null, "pubmed:20448148", null, "MZago2 mutant Y\u039490", "GSM540646", null, "tissue:48hpf embryo  MZago2 mutant|strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:MZago2 \u039490/\u039490", "MZago2 mutant Y\u039490", "Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file.", "48hpf embryo  MZago2 mutant", null, "Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly  total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5\u2019 and 3\u2019 adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.", "Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf  embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen.", "strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:MZago2 \u039490/\u039490", "GSM540646", "GSM540646: MZago2 mutant Y\u039490", "GSM540646: MZago2 mutant Y\u039490", "GSM540646: MZago2 mutant Y\u039490", "1", null, "GEO Accession:GSM540646", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP002411", null, null, "Ago2_ydelta90.fastq", "fastq", 437752008.0, 12159778.0, "GSM540646 1", "0:36", "A:96750665;C:83495585;G:119239752;T:138073795;N:192211", 36, null, null, null, 96750665, 83495585, 119239752, 138073795, 192211, "SRX020028", "SRS066219", "SRA012683", "GEO", "Giraldez Lab, Genetics, Yale University", 1, 0.03964, null, 0.0, null, 0.99985, null, 0.00052, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2010-05-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36196, "SRR042433", "SRX020027", "SRS066218", "SRP002411", "PRJNA126003", "A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity", "GSE21503", "Transcriptome Analysis", "Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs  we sequenced  small RNAs in wild type  maternal zygotic dicer MZdicer and MZago2 mutants  using zebrafish as a model system. We find that  in contrast to other miRNAs  miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs  followed by uridylation and trimming  generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type  MZago2  MZdicer at 48 hpf", null, "pubmed:20448148", null, "WT2", "GSM540645", null, "tissue:48hpf embryo  WT|strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:wild type", "WT2", "Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file.", "48hpf embryo  WT", null, "Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly  total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5\u2019 and 3\u2019 adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.", "Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf  embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen.", "strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:wild type", "GSM540645", "GSM540645: WT2", "GSM540645: WT2", "GSM540645: WT2", "1", null, "GEO Accession:GSM540645", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP002411", null, null, "WT2.fastq", "fastq", 59530030.0, 1700858.0, "GSM540645 1", "0:35", "A:12981942;C:11521313;G:16378279;T:18609524;N:38972", 35, null, null, null, 12981942, 11521313, 16378279, 18609524, 38972, "SRX020027", "SRS066218", "SRA012683", "GEO", "Giraldez Lab, Genetics, Yale University", 1, 0.06435, null, 0.0, null, 0.99995, null, 0.0, null, 35, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2010-05-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36197, "SRR042432", "SRX020026", "SRS066217", "SRP002411", "PRJNA126003", "A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity", "GSE21503", "Transcriptome Analysis", "Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs  we sequenced  small RNAs in wild type  maternal zygotic dicer MZdicer and MZago2 mutants  using zebrafish as a model system. We find that  in contrast to other miRNAs  miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs  followed by uridylation and trimming  generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type  MZago2  MZdicer at 48 hpf", null, "pubmed:20448148", null, "MZdicer mutant2 hu896", "GSM540644", null, "tissue:48hpf embryo  Mzdicer mutant|strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu896/hu896", "MZdicer mutant2 hu896", "Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file.", "48hpf embryo  Mzdicer mutant", null, "Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly  total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5\u2019 and 3\u2019 adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.", "Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf  embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen.", "strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu896/hu896", "GSM540644", "GSM540644: MZdicer mutant2 hu896", "GSM540644: MZdicer mutant2 hu896", "GSM540644: MZdicer mutant2 hu896", "1", null, "GEO Accession:GSM540644", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP002411", null, null, "MZdicer2_hu896.fastq", "fastq", 4268740.0, 121964.0, "GSM540644 1", "0:35", "A:813936;C:1034356;G:1131604;T:1280756;N:8088", 35, null, null, null, 813936, 1034356, 1131604, 1280756, 8088, "SRX020026", "SRS066217", "SRA012683", "GEO", "Giraldez Lab, Genetics, Yale University", 1, 0.03836, null, 0.0009, null, 0.99849, null, 0.3021, null, 35, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2010-05-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36198, "SRR042431", "SRX020025", "SRS066216", "SRP002411", "PRJNA126003", "A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity", "GSE21503", "Transcriptome Analysis", "Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs  we sequenced  small RNAs in wild type  maternal zygotic dicer MZdicer and MZago2 mutants  using zebrafish as a model system. We find that  in contrast to other miRNAs  miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs  followed by uridylation and trimming  generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type  MZago2  MZdicer at 48 hpf", null, "pubmed:20448148", null, "WT1", "GSM540643", null, "tissue:48hpf embryo  WT|strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:wild type", "WT1", "Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file.", "48hpf embryo  WT", null, "Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly  total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5\u2019 and 3\u2019 adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.", "Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf  embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen.", "strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:wild type", "GSM540643", "GSM540643: WT1", "GSM540643: WT1", "GSM540643: WT1", "1", null, "GEO Accession:GSM540643", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP002411", null, "quality book char:@|quality scoring system:log odds", "WT1.fastq", "fastq", 26959392.0, 748872.0, "GSM540643 1", "0:36", "A:6097309;C:6093948;G:6950185;T:7813829;N:4121", 36, null, null, null, 6097309, 6093948, 6950185, 7813829, 4121, "SRX020025", "SRS066216", "SRA012683", "GEO", "Giraldez Lab, Genetics, Yale University", 1, 0.0022, null, 0.0, null, 0.99993, null, 0.0, null, 36, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2010-05-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36199, "SRR042430", "SRX020024", "SRS066215", "SRP002411", "PRJNA126003", "A novel miRNA processing pathway independent of Dicer requires Argonaute2 catalytic activity", "GSE21503", "Transcriptome Analysis", "Here we identify a Dicer independent miRNA biogenesis pathway that employs the slicer catalytic activity of Argonaute2 Ago2. To uncover Dicer independent miRNAs  we sequenced  small RNAs in wild type  maternal zygotic dicer MZdicer and MZago2 mutants  using zebrafish as a model system. We find that  in contrast to other miRNAs  miR 451 levels were increased in MZdicer but drastically reduced in the MZago2 mutants. We show that pre miR 451 processing requires Ago2 catalytic activity in vivo. MZago2 mutant embryos display delayed erythrocyte maturation that can be rescued by wild type Ago2 or miR 451 duplex but not catalytically dead Ago2. We propose that Ago2 mediated cleavage of a subset of pre miRNAs  followed by uridylation and trimming  generates functional miRNAs in a Dicer independent manner. Overall design: Examination of small RNAs 18 to 35 nucleotides in 3 different zebrafish genotypes wild type  MZago2  MZdicer at 48 hpf", null, "pubmed:20448148", null, "MZdicer mutant1 hu715", "GSM540642", null, "tissue:48hpf embryo  Mzdicer mutant|strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu715/hu715", "MZdicer mutant1 hu715", "Alignment: Sequence reads were mapped to Zebrafish Zv8/danRer6 precursor miRNA sequences using Bowtie software version 0.12.1 with maximal two mismatches within first 20 nucleotides. Alignments are available in the supplementary *out.txt file.", "48hpf embryo  Mzdicer mutant", null, "Total RNA from frozen embryos was extracted with Trizol reagent and phenol/chloroform. Libraries were prepared according to Illumina's instructions Part # 1004239 Rev. A accompanying the small RNA Sample Kit. Briefly  total RNA samples were run in a denaturing PAGE and the band corresponding to the RNAs of 18 35 nucletides was excised. RNA 5\u2019 and 3\u2019 adapters were ligated sequentially. Reverse transcription followed by PCR amplified cDNA constructs with both adapters. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.", "Embryos were collected from breeding tanks and kept at 28C in p60 plates with water and 0.2 mg/L methylene blue. At 48 hpf  embryos were hand dechorionated and 40 embryos per sample were flash frozen in liquid nitrogen.", "strain:mixed AB  TU  TL TLF background|developmental stage:48hpf embryo|genotype:MZdicer hu715/hu715", "GSM540642", "GSM540642: MZdicer mutant1 hu715", "GSM540642: MZdicer mutant1 hu715", "GSM540642: MZdicer mutant1 hu715", "1", null, "GEO Accession:GSM540642", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP002411", null, "quality book char:@|quality scoring system:log odds", "MZdicer1_hu715.fastq", "fastq", 11972772.0, 332577.0, "GSM540642 1", "0:36", "A:2703131;C:3062840;G:3338413;T:2867600;N:788", 36, null, null, null, 2703131, 3062840, 3338413, 2867600, 788, "SRX020024", "SRS066215", "SRA012683", "GEO", "Giraldez Lab, Genetics, Yale University", 1, 0.00678, null, 0.00073, null, 0.99847, null, 0.3421, null, 36, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2010-05-04", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36278, "SRR352486", "SRX100938", "SRS266977", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "3P Seq Adult", "GSM813764", null, "source name:mixed gender adults|tissue:whole adult|developmental stage:mixed gender adults|genotype:wt", "3P Seq Adult", "Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924", "mixed gender adults", "For adult fish  anesthetized fish were homogenized in the TissueRuptor Qiagen. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html", "Zebrafish embryos or adults grown under standard condition", "tissue:whole adult|developmental stage:mixed gender adults|genotype:wt", "GSM813764", "GSM813764: 3P Seq Adult", "GSM813764: 3P Seq Adult", "GSM813764: 3P Seq Adult", "1", null, "GEO Accession:GSM813764", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "3P_Seq_Adult.fastq", "fastq", 824962572.0, 22915627.0, "GSM813764 1", "0:36", "A:230176177;C:144743199;G:130818857;T:314618483;N:4605856", 36, null, null, null, 230176177, 144743199, 130818857, 314618483, 4605856, "SRX100938", "SRS266977", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", 1, 0.64306, null, 0.03985, null, 0.78102, null, 0.46237, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "3prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Adult", "Adult", "Whole Organism", "All anatomical structures"], [36279, "SRR352485", "SRX100937", "SRS266976", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "3P Seq 72 hpf", "GSM813763", null, "tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf", "3P Seq 72 hpf", "Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. GSE24924", "whole embryo at 72 hpf", "Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html", "Zebrafish embryos or adults grown under standard condition", "tissue:whole embryo|developmental stage:72 hpf", "GSM813763", "GSM813763: 3P Seq 72 hpf", "GSM813763: 3P Seq 72 hpf", "GSM813763: 3P Seq 72 hpf", "1", null, "GEO Accession:GSM813763", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "3P_Seq_72hpf.fastq", "fastq", 875542968.0, 24320638.0, "GSM813763 1", "0:36", "A:246098313;C:139311840;G:129654215;T:353566279;N:6912321", 36, null, null, null, 246098313, 139311840, 129654215, 353566279, 6912321, "SRX100937", "SRS266976", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", 1, 0.72092, null, 0.09355, null, 0.7601, null, 0.4422, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "3prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [36280, "SRR352484", "SRX100936", "SRS266975", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "3P Seq 24 hpf", "GSM813762", null, "tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf", "3P Seq 24 hpf", "Reads were reverse complemented and aligned to the D. rerio genome Zv9/danRer7 using Bowtie. Reads that aligned to up to four genomic locus and had one or more mismatches at their three prime end within a terminal adenylate run were carried forward as 3P tags. Reads mapping to the same locus with the same number of terminal adenylates were consolidated in the processed data file. The BED file is as in Jan et al. GSE24924", "whole embryo at 24 hpf", "Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "3P Seq; see http://web.wi.mit.edu/bartel/pub/protocols.html", "Zebrafish embryos or adults grown under standard condition", "tissue:whole embryo|developmental stage:24 hpf", "GSM813762", "GSM813762: 3P Seq 24 hpf", "GSM813762: 3P Seq 24 hpf", "GSM813762: 3P Seq 24 hpf", "1", null, "GEO Accession:GSM813762", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "3P_Seq_24hpf.fastq", "fastq", 951095592.0, 26419322.0, "GSM813762 1", "0:36", "A:261158914;C:169001356;G:163312440;T:350565754;N:7057128", 36, null, null, null, 261158914, 169001356, 163312440, 350565754, 7057128, "SRX100936", "SRS266975", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", null, null, null, null, null, null, null, null, null, null, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "3prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36281, "SRR352482", "SRX100935", "SRS266974", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "Strand specific RNA Seq 72 hpf", "GSM813761", null, "tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf", "Strand specific RNA Seq 72 hpf", "Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.", "whole embryo at 72 hpf", "Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992", "Zebrafish embryos or adults grown under standard condition", "tissue:whole embryo|developmental stage:72 hpf", "GSM813761", "GSM813761: Strand specific RNA Seq 72 hpf", "GSM813761: Strand specific RNA Seq 72 hpf", "GSM813761: Strand specific RNA Seq 72 hpf", "1", null, "GEO Accession:GSM813761", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "RNA_Seq_72hpf.1.fastq", "fastq", 734147136.0, 20392976.0, "GSM813761 1", "0:36", "A:175662892;C:172216317;G:208650086;T:171852136;N:5765705", 36, null, null, null, 175662892, 172216317, 208650086, 171852136, 5765705, "SRX100935", "SRS266974", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", 1, 0.4603, null, 0.10593, null, 0.88274, null, 0.59195, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [36282, "SRR352483", "SRX100935", "SRS266974", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "Strand specific RNA Seq 72 hpf", "GSM813761", null, "tissue:whole embryo at 72 hpf embryo|developmental stage:72 hpf", "Strand specific RNA Seq 72 hpf", "Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.", "whole embryo at 72 hpf", "Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992", "Zebrafish embryos or adults grown under standard condition", "tissue:whole embryo|developmental stage:72 hpf", "GSM813761", "GSM813761: Strand specific RNA Seq 72 hpf", "GSM813761: Strand specific RNA Seq 72 hpf", "GSM813761: Strand specific RNA Seq 72 hpf", "1", null, "GEO Accession:GSM813761", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "RNA_Seq_72hpf.2.fastq", "fastq", 924879168.0, 25691088.0, "GSM813761 2", "0:36", "A:218871678;C:217000200;G:266487098;T:214411336;N:8108856", 36, null, null, null, 218871678, 217000200, 266487098, 214411336, 8108856, "SRX100935", "SRS266974", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", 1, 0.47296, null, 0.10988, null, 0.86397, null, 0.59423, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [36283, "SRR352480", "SRX100934", "SRS266973", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "Strand specific RNA Seq 24 hpf", "GSM813760", null, "tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf", "Strand specific RNA Seq 24 hpf", "Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.", "whole embryo at 24 hpf", "Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992", "Zebrafish embryos or adults grown under standard condition", "tissue:whole embryo|developmental stage:24 hpf", "GSM813760", "GSM813760: Strand specific RNA Seq 24 hpf", "GSM813760: Strand specific RNA Seq 24 hpf", "GSM813760: Strand specific RNA Seq 24 hpf", "1", null, "GEO Accession:GSM813760", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "RNA_Seq_24hpf.1.fastq", "fastq", 759129588.0, 21086933.0, "GSM813760 1", "0:36", "A:169759696;C:187766678;G:221392768;T:174382883;N:5827563", 36, null, null, null, 169759696, 187766678, 221392768, 174382883, 5827563, "SRX100934", "SRS266973", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", 1, 0.52959, null, 0.10037, null, 0.87014, null, 0.61896, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36284, "SRR352481", "SRX100934", "SRS266973", "SRP008845", "PRJNA146609", "Conserved Function of lincRNAs in Vertebrate Embryonic Development Despite Rapid Sequence Evolution", "GSE32880", "Other", "Thousands of large intervening non coding RNAs lincRNAs have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs  we used chromatin marks  polyA site mapping and RNA Seq data  to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs  only 29 had detectable sequence similarity with putative mammalian orthologs  typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without xxx sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation. Overall design: H3K4me3  H3K36me3 chromatin maps  3P Seq and RNA Seq were used to identify lincRNAs in the zebrafish genome", null, "pubmed:22196729", null, "Strand specific RNA Seq 24 hpf", "GSM813760", null, "tissue:whole embryo at 24 hpf embryo|developmental stage:24 hpf", "Strand specific RNA Seq 24 hpf", "Reads were aligned to the zebrafish danRer7 genome assembly using Bowtie  allowing for up to one mismatch and up to 4 genomic matches.", "whole embryo at 24 hpf", "Anesthetized 24 hpf and 72 hpf decorioneted embryos were washed three times in PBS 137 mM NaCl  2.7 mM KCl  1.5 mM KH2PO4  8 mM Na2HP04  pH 7.4 and suspended in PBS containing 1% freshly added formaldehyde. Embryos were transferred to a dounce homogenizer  dounced several times and incubated at room temperature for 15 min. Formaldehyde was quenched by adding 1/20 volume 2.5 M glycine. Cells were pelleted at 400 x g for 5 min. The supernatant was removed  and pellets were rinsed twice with PBS  flash frozen in liquid nitrogen and stored at \u201380C.", "polyA selected RNA was amplified using RiboAmp Plus RNA Amplification kit  randomly fragmented by partial alkaline hydrolysis. Size selected RNA fragments 25 45 nt were used for library preparation. Libraries were prepared as in Guo et al  2010 GSE21992", "Zebrafish embryos or adults grown under standard condition", "tissue:whole embryo|developmental stage:24 hpf", "GSM813760", "GSM813760: Strand specific RNA Seq 24 hpf", "GSM813760: Strand specific RNA Seq 24 hpf", "GSM813760: Strand specific RNA Seq 24 hpf", "1", null, "GEO Accession:GSM813760", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP008845", null, "read name barcode proc directive:ignore", "RNA_Seq_24hpf.2.fastq", "fastq", 916505136.0, 25458476.0, "GSM813760 2", "0:36", "A:203678661;C:227621613;G:269472018;T:207401580;N:8331264", 36, null, null, null, 203678661, 227621613, 269472018, 207401580, 8331264, "SRX100934", "SRS266973", "SRA047033", "GEO", "Whitehead Institute for Biomedical Research", 1, 0.54008, null, 0.10064, null, 0.85425, null, 0.61991, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-10-11", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36333, "SRR398324", "SRX115582", "SRS285699", "SRP010291", "PRJNA150927", "miR 221 is required for endothelial tip cell behaviors during vascular development", "GSE35078", "Transcriptome Analysis", "Through deep sequencing and functional screening in zebrafish  we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor.  Furthermore  miR 221 was required for tip cell proliferation and migration  as well as tip cell potential in mosaic blood vessels.  miR 221 knockdown also prevented \u201chyper angiogenesis\u201d defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling.  Finally  miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1.  These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells.", null, "pubmed:22340502", null, "kdrl:egfp min microRNA", "GSM861786", null, "tissue:FACS isolated egfp negative cells|genotype:Tgkdrl:egfp|age:24 hpf|development stage:embryo|cell type:non endothelial cells", "kdrl:egfp min microRNA", "The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2.", "FACS isolated egfp negative cells", "Tgkdrl:egfp embryos were dissociated at 24 hpf  followed by fluorescence activated cell sorting to isolate GFP positive and  negative cells.", "Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters  followed by cDNA synthesis and amplification with Illumina primers.", null, "genotype:Tgkdrl:egfp|age:24 hpf|developmental stage:embryo|cell type:non endothelial cells", "GSM861786", "GSM861786: kdrl:egfp min microRNA; Danio rerio; RNA Seq", "GSM861786 1", "GSM861786: kdrl:egfp min microRNA", "1", null, "GEO Accession:GSM861786", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP010291", null, null, "miRNA_GFP_MINUS.fastq.gz", "fastq", 206441460.0, 5734485.0, "GSM861786 r1", "0:36", "A:53061964;C:48186825;G:47161433;T:53484016;N:4547222", 36, null, null, null, 53061964, 48186825, 47161433, 53484016, 4547222, "SRX115582", "SRS285699", "SRA049243", "GEO", "Nathan Lawson Lab, PGFE, Umass Medical School", 1, 0.01499, null, 0.01416, null, 0.99922, null, 0.4, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-01-12", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36334, "SRR398323", "SRX115581", "SRS285698", "SRP010291", "PRJNA150927", "miR 221 is required for endothelial tip cell behaviors during vascular development", "GSE35078", "Transcriptome Analysis", "Through deep sequencing and functional screening in zebrafish  we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor.  Furthermore  miR 221 was required for tip cell proliferation and migration  as well as tip cell potential in mosaic blood vessels.  miR 221 knockdown also prevented \u201chyper angiogenesis\u201d defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling.  Finally  miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1.  These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells.", null, "pubmed:22340502", null, "kdrl:egfp pos microRNA", "GSM861785", null, "tissue:FACS isolated kdrl:egfp positive cells|genotype:Tgkdrl:egfp|age:24 hpf|development stage:embryo|cell type:endothelial cells", "kdrl:egfp pos microRNA", "The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2.", "FACS isolated kdrl:egfp positive cells", "Tgkdrl:egfp embryos were dissociated at 24 hpf  followed by fluorescence activated cell sorting to isolate GFP positive and  negative cells.", "Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters  followed by cDNA synthesis and amplification with Illumina primers.", null, "genotype:Tgkdrl:egfp|age:24 hpf|developmental stage:embryo|cell type:endothelial cells", "GSM861785", "GSM861785: kdrl:egfp pos microRNA; Danio rerio; RNA Seq", "GSM861785 1", "GSM861785: kdrl:egfp pos microRNA", "1", null, "GEO Accession:GSM861785", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP010291", null, null, "miRNA_GFP_PLUS.fastq.gz", "fastq", 265629096.0, 7378586.0, "GSM861785 r1", "0:36", "A:67563811;C:62134550;G:62283750;T:67966396;N:5680589", 36, null, null, null, 67563811, 62134550, 62283750, 67966396, 5680589, "SRX115581", "SRS285698", "SRA049243", "GEO", "Nathan Lawson Lab, PGFE, Umass Medical School", 1, 0.01356, null, 0.01279, null, 0.99924, null, 0.3125, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-01-12", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36482, "SRR530894", "SRX172598", "SRS352620", "SRP014646", "PRJNA171751", "MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]", "GSE39808", "Transcriptome Analysis", "Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing", "parent bioproject:PRJNA171747", "pubmed:22921993", null, "60hpf TCDD 3", "GSM979608", null, "source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD", "60hpf TCDD 3", "CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files", "Embryos", null, "Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.", null, "strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD", "GSM979608", "GSM979608: 60hpf TCDD 3; Danio rerio; RNA Seq", "GSM979608 1", "GSM979608: 60hpf TCDD 3", "1", null, "GEO Accession:GSM979608", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014646", null, null, null, null, 1007239870.0, 28778282.0, "GSM979608 r1", "0:35", "0:284531587;1:248579138;2:213782485;3:258771962;.:1574698", 35, null, null, null, null, null, null, null, null, "SRX172598", "SRS352620", "SRA056525", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.04824, null, 0.03, null, 0.981, null, 0.49967, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-08-01", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36483, "SRR530893", "SRX172597", "SRS352619", "SRP014646", "PRJNA171751", "MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]", "GSE39808", "Transcriptome Analysis", "Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing", "parent bioproject:PRJNA171747", "pubmed:22921993", null, "60hpf TCDD 2", "GSM979607", null, "source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD", "60hpf TCDD 2", "CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files", "Embryos", null, "Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.", null, "strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD", "GSM979607", "GSM979607: 60hpf TCDD 2; Danio rerio; RNA Seq", "GSM979607 1", "GSM979607: 60hpf TCDD 2", "1", null, "GEO Accession:GSM979607", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014646", null, null, "MH_0011.csfasta", "SOLiD_native", 407347325.0, 11638495.0, "GSM979607 r1", "0:35", "0:99062820;1:113921998;2:81336108;3:112422342;.:604057", 35, null, null, null, null, null, null, null, null, "SRX172597", "SRS352619", "SRA056525", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.04258, null, 0.02455, null, 0.98287, null, 0.5048, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-08-01", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36484, "SRR530892", "SRX172596", "SRS352618", "SRP014646", "PRJNA171751", "MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]", "GSE39808", "Transcriptome Analysis", "Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing", "parent bioproject:PRJNA171747", "pubmed:22921993", null, "60hpf TCDD 1", "GSM979606", null, "source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD", "60hpf TCDD 1", "CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files", "Embryos", null, "Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.", null, "strain:TL wild type|tissue:embryos|time:60 hpf|treatment:TCDD", "GSM979606", "GSM979606: 60hpf TCDD 1; Danio rerio; RNA Seq", "GSM979606 1", "GSM979606: 60hpf TCDD 1", "1", null, "GEO Accession:GSM979606", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014646", null, null, "MH_0010.csfasta", "SOLiD_native", 680837045.0, 19452487.0, "GSM979606 r1", "0:35", "0:165079839;1:167219862;2:147812329;3:199659766;.:1065249", 35, null, null, null, null, null, null, null, null, "SRX172596", "SRS352618", "SRA056525", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.02295, null, 0.01479, null, 0.98884, null, 0.55191, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-08-01", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36485, "SRR530891", "SRX172595", "SRS352617", "SRP014646", "PRJNA171751", "MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]", "GSE39808", "Transcriptome Analysis", "Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing", "parent bioproject:PRJNA171747", "pubmed:22921993", null, "60hpf DMSO 3", "GSM979605", null, "source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO", "60hpf DMSO 3", "CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files", "Embryos", null, "Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.", null, "strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO", "GSM979605", "GSM979605: 60hpf DMSO 3; Danio rerio; RNA Seq", "GSM979605 1", "GSM979605: 60hpf DMSO 3", "1", null, "GEO Accession:GSM979605", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014646", null, null, "MH_0009.csfasta", "SOLiD_native", 495019840.0, 14143424.0, "GSM979605 r1", "0:35", "0:134854583;1:126192934;2:102458221;3:130747961;.:766141", 35, null, null, null, null, null, null, null, null, "SRX172595", "SRS352617", "SRA056525", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.06707, null, 0.04409, null, 0.97285, null, 0.5058, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-08-01", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36486, "SRR530890", "SRX172594", "SRS352616", "SRP014646", "PRJNA171751", "MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]", "GSE39808", "Transcriptome Analysis", "Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing", "parent bioproject:PRJNA171747", "pubmed:22921993", null, "60hpf DMSO 2", "GSM979604", null, "source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO", "60hpf DMSO 2", "CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files", "Embryos", null, "Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.", null, "strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO", "GSM979604", "GSM979604: 60hpf DMSO 2; Danio rerio; RNA Seq", "GSM979604 1", "GSM979604: 60hpf DMSO 2", "1", null, "GEO Accession:GSM979604", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014646", null, null, "MH_0008.qual", "SOLiD_native", 440403425.0, 12582955.0, "GSM979604 r1", "0:35", "0:110302240;1:106481197;2:104551283;3:118415637;.:653068", 35, null, null, null, null, null, null, null, null, "SRX172594", "SRS352616", "SRA056525", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.05778, null, 0.03522, null, 0.97423, null, 0.50884, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-08-01", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36487, "SRR530889", "SRX172593", "SRS352615", "SRP014646", "PRJNA171751", "MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]", "GSE39808", "Transcriptome Analysis", "Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing", "parent bioproject:PRJNA171747", "pubmed:22921993", null, "60hpf DMSO 1", "GSM979603", null, "source name:Embryos|strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO", "60hpf DMSO 1", "CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files", "Embryos", null, "Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.", null, "strain:TL wild type|tissue:embryos|time:60 hpf|treatment:DMSO", "GSM979603", "GSM979603: 60hpf DMSO 1; Danio rerio; RNA Seq", "GSM979603 1", "GSM979603: 60hpf DMSO 1", "1", null, "GEO Accession:GSM979603", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014646", null, null, "MH_0007.csfasta MH_0007.qual", "SOLiD_native SOLiD_native", 583800490.0, 16680014.0, "GSM979603 r1", "0:35", "0:166122108;1:149534173;2:111986455;3:155255262;.:902492", 35, null, null, null, null, null, null, null, null, "SRX172593", "SRS352615", "SRA056525", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.05644, null, 0.03829, null, 0.9781, null, 0.4997, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-08-01", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36488, "SRR530888", "SRX172592", "SRS352614", "SRP014646", "PRJNA171751", "MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]", "GSE39808", "Transcriptome Analysis", "Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing", "parent bioproject:PRJNA171747", "pubmed:22921993", null, "36hpf TCDD 3", "GSM979602", null, "source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD", "36hpf TCDD 3", "CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files", "Embryos", null, "Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.", null, "strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD", "GSM979602", "GSM979602: 36hpf TCDD 3; Danio rerio; RNA Seq", "GSM979602 1", "GSM979602: 36hpf TCDD 3", "1", null, "GEO Accession:GSM979602", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014646", null, null, "MH_0006.qual MH_0006.csfasta", "SOLiD_native SOLiD_native", 214059615.0, 6115989.0, "GSM979602 r1", "0:35", "0:56635752;1:54053300;2:48355842;3:54677354;.:337367", 35, null, null, null, null, null, null, null, null, "SRX172592", "SRS352614", "SRA056525", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.13044, null, 0.07694, null, 0.95704, null, 0.53005, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36489, "SRR530887", "SRX172591", "SRS352613", "SRP014646", "PRJNA171751", "MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]", "GSE39808", "Transcriptome Analysis", "Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing", "parent bioproject:PRJNA171747", "pubmed:22921993", null, "36hpf TCDD 2", "GSM979601", null, "source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD", "36hpf TCDD 2", "CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files", "Embryos", null, "Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.", null, "strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD", "GSM979601", "GSM979601: 36hpf TCDD 2; Danio rerio; RNA Seq", "GSM979601 1", "GSM979601: 36hpf TCDD 2", "1", null, "GEO Accession:GSM979601", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014646", null, null, null, null, 388475115.0, 11099289.0, "GSM979601 r1", "0:35", "0:103611863;1:99408831;2:86592980;3:98238344;.:623097", 35, null, null, null, null, null, null, null, null, "SRX172591", "SRS352613", "SRA056525", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.15634, null, 0.10763, null, 0.96069, null, 0.47755, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36490, "SRR530886", "SRX172590", "SRS352612", "SRP014646", "PRJNA171751", "MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]", "GSE39808", "Transcriptome Analysis", "Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing", "parent bioproject:PRJNA171747", "pubmed:22921993", null, "36hpf TCDD 1", "GSM979600", null, "source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD", "36hpf TCDD 1", "CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files", "Embryos", null, "Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.", null, "strain:TL wild type|tissue:embryos|time:36 hpf|treatment:TCDD", "GSM979600", "GSM979600: 36hpf TCDD 1; Danio rerio; RNA Seq", "GSM979600 1", "GSM979600: 36hpf TCDD 1", "1", null, "GEO Accession:GSM979600", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014646", null, null, "MH_0004.csfasta", "SOLiD_native", 366389765.0, 10468279.0, "GSM979600 r1", "0:35", "0:100797199;1:91391785;2:80412155;3:93217840;.:570786", 35, null, null, null, null, null, null, null, null, "SRX172590", "SRS352612", "SRA056525", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.14106, null, 0.09874, null, 0.95724, null, 0.49685, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36491, "SRR530885", "SRX172589", "SRS352611", "SRP014646", "PRJNA171751", "MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]", "GSE39808", "Transcriptome Analysis", "Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing", "parent bioproject:PRJNA171747", "pubmed:22921993", null, "36hpf DMSO 3", "GSM979599", null, "source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO", "36hpf DMSO 3", "CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files", "Embryos", null, "Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.", null, "strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO", "GSM979599", "GSM979599: 36hpf DMSO 3; Danio rerio; RNA Seq", "GSM979599 1", "GSM979599: 36hpf DMSO 3", "1", null, "GEO Accession:GSM979599", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014646", null, null, "MH_0003.csfasta", "SOLiD_native", 2108864835.0, 60253281.0, "GSM979599 r1", "0:35", "0:591489585;1:461028640;2:379338654;3:673048278;.:3959678", 35, null, null, null, null, null, null, null, null, "SRX172589", "SRS352611", "SRA056525", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.09321, null, 0.06563, null, 0.98244, null, 0.50577, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36492, "SRR530884", "SRX172588", "SRS352610", "SRP014646", "PRJNA171751", "MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]", "GSE39808", "Transcriptome Analysis", "Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing", "parent bioproject:PRJNA171747", "pubmed:22921993", null, "36hpf DMSO 2", "GSM979598", null, "source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO", "36hpf DMSO 2", "CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files", "Embryos", null, "Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.", null, "strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO", "GSM979598", "GSM979598: 36hpf DMSO 2; Danio rerio; RNA Seq", "GSM979598 1", "GSM979598: 36hpf DMSO 2", "1", null, "GEO Accession:GSM979598", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014646", null, null, "MH_0002.qual", "SOLiD_native", 363765885.0, 10393311.0, "GSM979598 r1", "0:35", "0:99316622;1:92947128;2:80099367;3:90839592;.:563176", 35, null, null, null, null, null, null, null, null, "SRX172588", "SRS352610", "SRA056525", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.13435, null, 0.09839, null, 0.96146, null, 0.49914, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36493, "SRR530883", "SRX172587", "SRS352609", "SRP014646", "PRJNA171751", "MicroRNA expression profiling post short term exposure to TCDD in zebrafish embryos [miRNA Seq data]", "GSE39808", "Transcriptome Analysis", "Although many drugs and environmental chemicals are teratogenic  the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs miRNAs   single stranded RNA molecules of 22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation  are important regulators of a variety of cellular processes including embryonic development and cellular differentiation.  We hypothesized that exposure to xenobiotics can alter miRNA expression and contribute to the mechanisms by which environmental chemicals disrupt embryonic development. To test this hypothesis for one well known teratogen  we exposed zebrafish embryos to DMSO 0.1% or TCDD 5 nM for 1 hr at 30 hpf and measured microRNA expression using several methods at 36 hpf and 60 hpf. TCDD caused strong induction of CYP1A at 36 hpf 62 fold and 60 hpf 135 fold as determined by qPCR  verifying the  effectiveness of the exposure.  microRNA expression profiles were determined using microarrays Agilent and Exiqon  next generation sequencing SOLiD and real time RT PCR. The two microarray platforms yielded results that were similar but not identical; both showed significant changes in expression of miR 451  23a  23b  24 and 27e at 60 hpf.  Multiple analyses were performed on the SOLiD sequences yielding a total of 16 miRNAs as potentially differentially expressed by TCDD in zebrafish embryos.  However  miR 27e was the only miRNA to be identified as differentially expressed by all three methods both microarrays  SOLiD sequencing  and qPCR.  These results suggest that TCDD exposure causes modest changes in expression of microRNAs  including some miR 451  23a  23b  24 and 27e that are critical for hematopoiesis and cardiovascular development. Overall design: Small RNA profiles were deteremined in TCDD exposed zebrafish embryos using SOLID sequencing", "parent bioproject:PRJNA171747", "pubmed:22921993", null, "36hpf DMSO 1", "GSM979597", null, "source name:Embryos|strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO", "36hpf DMSO 1", "CLC Bio Genomics Work bench version 4.7 was used Adaptor trimming followed by alignining the reads to precursor miRNA sequences downloaded from miRBASE v.16. Remaining reads were mapped to other non coding RNAs downloaded from ncRNA.org Statistical analysis was done using edgeR  a bioconductor package R project Genome build: miRBase version 16 Supplementary files format and content: tab delimited text files", "Embryos", null, "Small RNA libraries were prepared using the small RNA expression kit SREK protocol Applied Biosystems  Foster City  CA. Sequencing was done on a SOLiD V3 system Applied Biosystems.", null, "strain:TL wild type|tissue:embryos|time:36 hpf|treatment:DMSO", "GSM979597", "GSM979597: 36hpf DMSO 1; Danio rerio; RNA Seq", "GSM979597 1", "GSM979597: 36hpf DMSO 1", "1", null, "GEO Accession:GSM979597", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ABI_SOLID", "AB SOLiD System 3.0", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>35</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP014646", null, null, "MH_0001F3.csfasta MH_0001F3_QV.qual", "SOLiD_native SOLiD_native", 309659000.0, 8847400.0, "GSM979597 r1", "0:35", "0:83729307;1:78100521;2:70827559;3:76531823;.:469790", 35, null, null, null, null, null, null, null, null, "SRX172587", "SRS352609", "SRA056525", "GEO", "Aluru Lab, Biology, Woods Hole Oceanographic Institution", 1, 0.56398, null, 0.33182, null, 0.91092, null, 0.5842, null, 35, null, "B", null, "usable mapping rate", "legacy", "early", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-08-01", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [36731, "SRR836199", "SRX272888", "SRS417394", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq 5dpf", "GSM1131537", null, "tissue:Whole embryos|developmental stage:5 dpf molecule:ribosome footprinted RNA", "20120724 RPF Seq 5dpf", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:5 dpf molecule:ribosome footprinted RNA", "GSM1131537", "GSM1131537: 20120724 RPF Seq 5dpf; Danio rerio; RNA Seq", "GSM1131537 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131537", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_5dpf.fastq.gz", "fastq", 5339394852.0, 121349883.0, "GSM1131537 r1", "0:44", "A:993131212;C:1552513636;G:1792926993;T:1000757523;N:65488", 44, null, null, null, 993131212, 1552513636, 1792926993, 1000757523, 65488, "SRX272888", "SRS417394", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.04708, null, 0.00988, null, 0.99774, null, 0.7502, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Larval", "Larval", "Whole Organism", "All anatomical structures"], [36732, "SRR836198", "SRX272887", "SRS417393", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq 28hpf", "GSM1131536", null, "tissue:Whole embryos|developmental stage:28 hpf molecule:ribosome footprinted RNA", "20120724 RPF Seq 28hpf", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:28 hpf molecule:ribosome footprinted RNA", "GSM1131536", "GSM1131536: 20120724 RPF Seq 28hpf; Danio rerio; RNA Seq", "GSM1131536 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131536", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_28hpf.fastq.gz", "fastq", 5844769480.0, 132835670.0, "GSM1131536 r1", "0:44", "A:967687923;C:1803414766;G:2048220630;T:1024594100;N:852061", 44, null, null, null, 967687923, 1803414766, 2048220630, 1024594100, 852061, "SRX272887", "SRS417393", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.054, null, 0.00377, null, 0.99762, null, 0.77752, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [36733, "SRR836197", "SRX272886", "SRS417392", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq Bud", "GSM1131535", null, "tissue:Whole embryos|developmental stage:Bud|strain:TL/AB|target molecule:ribosome footprinted RNA", "20120724 RPF Seq Bud", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:Bud|strain:TL/AB|target molecule:ribosome footprinted RNA", "GSM1131535", "GSM1131535: 20120724 RPF Seq Bud; Danio rerio; RNA Seq", "GSM1131535 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131535", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_Bud.fastq.gz", "fastq", 5245678988.0, 119219977.0, "GSM1131535 r1", "0:44", "A:785136766;C:1705642298;G:1892015387;T:862815185;N:69352", 44, null, null, null, 785136766, 1705642298, 1892015387, 862815185, 69352, "SRX272886", "SRS417392", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.0214, null, 0.00105, null, 0.99823, null, 0.906, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Undetermined", "Embryo", "Whole Organism", "All anatomical structures"], [36734, "SRR836196", "SRX272885", "SRS417391", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq Shield", "GSM1131534", null, "tissue:Whole embryos|developmental stage:Shield|strain:TL/AB|target molecule:ribosome footprinted RNA", "20120724 RPF Seq Shield", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:Shield|strain:TL/AB|target molecule:ribosome footprinted RNA", "GSM1131534", "GSM1131534: 20120724 RPF Seq Shield; Danio rerio; RNA Seq", "GSM1131534 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131534", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_Shield.fastq.gz", "fastq", 5407148516.0, 122889739.0, "GSM1131534 r1", "0:44", "A:1112688703;C:1598204601;G:1639649897;T:1055648833;N:956482", 44, null, null, null, 1112688703, 1598204601, 1639649897, 1055648833, 956482, "SRX272885", "SRS417391", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.01533, null, 0.0016, null, 0.99864, null, 0.73416, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Gastrula", "Embryo", "Whole Organism", "All anatomical structures"], [36735, "SRR836195", "SRX272884", "SRS417390", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq Dome", "GSM1131533", null, "tissue:Whole embryos|developmental stage:Dome|strain:TL/AB|target molecule:ribosome footprinted RNA", "20120724 RPF Seq Dome", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:Dome|strain:TL/AB|target molecule:ribosome footprinted RNA", "GSM1131533", "GSM1131533: 20120724 RPF Seq Dome; Danio rerio; RNA Seq", "GSM1131533 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131533", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_Dome.fastq.gz", "fastq", 5455941832.0, 123998678.0, "GSM1131533 r1", "0:44", "A:1174530251;C:1596486361;G:1605087499;T:1077423125;N:2414596", 44, null, null, null, 1174530251, 1596486361, 1605087499, 1077423125, 2414596, "SRX272884", "SRS417390", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.00739, null, 0.0007, null, 0.99898, null, 0.86907, null, 44, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [36736, "SRR836194", "SRX272883", "SRS417389", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq 1KCell", "GSM1131532", null, "tissue:Whole embryos|developmental stage:1k cells|strain:TL/AB|target molecule:ribosome footprinted RNA", "20120724 RPF Seq 1KCell", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:1k cells|strain:TL/AB|target molecule:ribosome footprinted RNA", "GSM1131532", "GSM1131532: 20120724 RPF Seq 1KCell; Danio rerio; RNA Seq", "GSM1131532 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131532", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_1KCell.fastq.gz", "fastq", 6177670620.0, 140401605.0, "GSM1131532 r1", "0:44", "A:1115906097;C:1874096579;G:1974799887;T:1211772717;N:1095340", 44, null, null, null, 1115906097, 1874096579, 1974799887, 1211772717, 1095340, "SRX272883", "SRS417389", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.02237, null, 0.00392, null, 0.99847, null, 0.87194, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [36737, "SRR836193", "SRX272882", "SRS417388", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq 256Cell", "GSM1131531", null, "tissue:Whole embryos|developmental stage:256 cells|strain:TL/AB|target molecule:ribosome footprinted RNA", "20120724 RPF Seq 256Cell", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:256 cells|strain:TL/AB|target molecule:ribosome footprinted RNA", "GSM1131531", "GSM1131531: 20120724 RPF Seq 256Cell; Danio rerio; RNA Seq", "GSM1131531 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131531", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_256Cell.fastq.gz", "fastq", 5883566700.0, 133717425.0, "GSM1131531 r1", "0:44", "A:1010263447;C:1822722383;G:1960819573;T:1088614485;N:1146812", 44, null, null, null, 1010263447, 1822722383, 1960819573, 1088614485, 1146812, "SRX272882", "SRS417388", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.02862, null, 0.0036, null, 0.99837, null, 0.90559, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Blastula", "Embryo", "Whole Organism", "All anatomical structures"], [36738, "SRR836192", "SRX272881", "SRS417387", "SRP021915", "PRJNA200706", "Ribosome Profiling over a Zebrafish Developmental Timecourse", "GSE46512", "Transcriptome Analysis", "To experimentally validate the non coding status of annotated lncRNAs  we performed ribosome profiling over a developmental timecourse that matched our previously published Pauli et al. 2012 developmental transcriptome. We find that many previously annotated lncRNAs appear to be translated  but in a pattern more akin to five prime' leaders of coding genes. Overall design: Ribosome profiling over 8 stages in early zebrafish development: 2 4 cell  256 cell  1K cell  Dome  Shield  Bud  28hpf and 5dpf", null, "pubmed:23698349", null, "20120724 RPF Seq 2 4Cell", "GSM1131530", null, "tissue:Whole embryos|developmental stage:2 4 cells|strain:TL/AB|target molecule:ribosome footprinted RNA", "20120724 RPF Seq 2 4Cell", "Adapters trimmed using custom script Reads that mapped to zebrafish rRNAs SILVA rRNA database: http://www.arb silva.de/ by Bowtie2  N 1  L 20  k 20 were discarded Remaining reads mapped to previously assembled zebrafish developmental transcriptome Pauli et al. 2012 on top of the Zv9/danRer7 assembly of the zebrafish genome by Tophat2; no indels  no novel junctions   M  g 10 Only RPFs of length 27nt to 32nt used. P site positions determined to be +12 for 27 28nt RPFs  +13 for 29 31nt RPFs  +13 for 29 31nt RPFs  +14 for 32nt RPFs. Custom scripts used to generate bw files of genome wide ribosome profiles corresponding to P site occupancy  in conjunction with BedTools and UCSC bedgraphToBedBed Genome build: Zv9 danRer7 Supplementary files format and content: bigwig files corresponding to P site occupancy by ribosomes", "Whole embryos", "Embryos were quickly washed in ice cold PBS and flash frozen in liquid nitrogen", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "400 600 embryos per stage from TL/AB WT strains were allowed to grow at 28.5\u00b0C and staged according to Kimmel et al. Dev. Dyn. 1995", "developmental stage:2 4 cells|strain:TL/AB|target molecule:ribosome footprinted RNA", "GSM1131530", "GSM1131530: 20120724 RPF Seq 2 4Cell; Danio rerio; RNA Seq", "GSM1131530 1", null, "1", "Embryos were lysed by repeated micropipetting in 1.5ml of cold polysome buffer 20 mM Tris HCl pH 7.4  250 mM NaCl  15 mM MgCl2  1mM dithiothreitol  100 \u03bcg/ml cycloheximide with added 0.5% Triton X 100  500 \u03bcg/ml GMP PNP  24 U/ml TurboDNase Ambion AM2238  incubated with agitation for 10 min at 4\u00b0C  and clarified by centrifugation at 1300 rcf for 10 min at 4\u00b0C. 20\u03bcl RNAseI Ambion AM2294 was added to the 1.5 ml of supernatant and incubated for 30 min at 37\u00b0C  then stopped by chilling on ice and addition of 40 \u03bcl of SuperaseIn Ambion AM2694. Footprinted samples were pelleted through a sucrose cushion 1M sucrose in polysome buffer with added 100 U/ml SuperaseIn by centrifugation at 260 000 rcf for 4.5 hours at 4\u00b0C  and resuspended in 800 \u03bcl 10mM Tris pH 7.4 with 1% SDS. RNA was purified by hot acid phenol/chloroform extraction and precipitated by standard ethanol precipitation. Libraries were prepared essentially as described by Ingolia et al. Cell 2011", "GEO Accession:GSM1131530", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP021915", null, null, "20120724_RPF-Seq_2-4Cell.fastq.gz", "fastq", 1568173420.0, 35640305.0, "GSM1131530 r1", "0:44", "A:256220962;C:489258424;G:538563811;T:283859833;N:270390", 44, null, null, null, 256220962, 489258424, 538563811, 283859833, 270390, "SRX272881", "SRS417387", "SRA075002", "GEO", "Schier, Dept of Molecular and Cellular Biology, Harvard University", 1, 0.0297, null, 0.00558, null, 0.99821, null, 0.89066, null, 44, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2013-04-30", "Cleavage", "Embryo", "Whole Organism", "All anatomical structures"], [37121, "SRR952244", "SRX334986", "SRS469877", "SRP028754", "PRJNA214896", "Danio rerio Transcriptome or Gene expression", "PRJNA214896", "Other", "During early vertebrate development  various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.", null, null, "embryonic development", "General Sample for zebrafish", "1 cell", null, "breed:wild type zebrafish", null, null, null, null, null, null, null, null, "1 cell developmental stage of zebrafish", "1 cell", "1", "Zebrafish embryos were collected at 1 cell 0.2 hpf  16 cell 1.5 hpf  512 cell 2.75 hpf  oblong 3.7 hpf  5.3 hpf 50% epibody  6 somite 12 hpf  24 hpf day1 hpf and 48 hpf day2 stages. Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels  and small RNAs were isolated and purified. Subsequently  small RNAs were ligated with both a 5\u2019 adapter and 3\u2019 adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that  the reverse transcribed product  cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec  followed by 15 cycles consisting of 10 sec at 98 oC  15 sec at 72 oC  and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels  the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>44</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP028754", null, null, "s1-cell.fq", "fastq", 1002077048.0, 20450552.0, "1 cell", "0:49 1:0", "A:210178307;C:226566574;G:255003953;T:310259058;N:69156", 49, 0, null, null, 210178307, 226566574, 255003953, 310259058, 69156, "SRX334986", "SRS469877", "SRA097312", "Huazhong University of Science and Technology|CUCKOO", "Huazhong University of Science and Technology", 1, 0.0001, null, 3e-05, null, 0.99977, null, 0.58333, null, 49, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2014-08-12", "Multi-stage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [37122, "SRR953569", "SRX336211", "SRS470740", "SRP028862", "PRJNA215266", "Danio rerio Transcriptome or Gene expression", "PRJNA215266", "Other", "During early vertebrate development  various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.", null, null, "small RNA sequencing for zebrafish early development", "General Sample for zebrafish", "zebrafish early development", null, "breed:wild type zebrafish", null, null, null, null, null, null, null, null, "48hpf of zebrafish development", "48hpf stage", "1", "Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels  and small RNAs were isolated and purified. Subsequently  small RNAs were ligated with both a 5\u2019 adapter and 3\u2019 adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that  the reverse transcribed product  cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec  followed by 15 cycles consisting of 10 sec at 98 oC  15 sec at 72 oC  and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels  the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP028862", null, null, "day2.fq", "fastq", 628342631.0, 12823319.0, "48hpf", "0:49", "A:148145336;C:136573491;G:166351863;T:177234943;N:36998", 49, null, null, null, 148145336, 136573491, 166351863, 177234943, 36998, "SRX336211", "SRS470740", "SRA098041", "Huazhong University of Science and Technology|cuckoo", "Huazhong University of Science and Technology", 1, 1e-05, null, 0.0, null, 0.99997, null, 1.0, null, 49, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-07-22", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [37123, "SRR953568", "SRX336209", "SRS470740", "SRP028862", "PRJNA215266", "Danio rerio Transcriptome or Gene expression", "PRJNA215266", "Other", "During early vertebrate development  various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.", null, null, "small RNA sequencing for zebrafish early development", "General Sample for zebrafish", "zebrafish early development", null, "breed:wild type zebrafish", null, null, null, null, null, null, null, null, "24hpf of zebrafish development", "24hpf stage", "1", "Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels  and small RNAs were isolated and purified. Subsequently  small RNAs were ligated with both a 5\u2019 adapter and 3\u2019 adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that  the reverse transcribed product  cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec  followed by 15 cycles consisting of 10 sec at 98 oC  15 sec at 72 oC  and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels  the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP028862", null, null, "day1.fq", "fastq", 575258726.0, 11739974.0, "24hpf", "0:49", "A:132961290;C:123570971;G:152269421;T:166422672;N:34372", 49, null, null, null, 132961290, 123570971, 152269421, 166422672, 34372, "SRX336209", "SRS470740", "SRA098041", "Huazhong University of Science and Technology|cuckoo", "Huazhong University of Science and Technology", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 49, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-07-22", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [37124, "SRR953567", "SRX336208", "SRS470740", "SRP028862", "PRJNA215266", "Danio rerio Transcriptome or Gene expression", "PRJNA215266", "Other", "During early vertebrate development  various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.", null, null, "small RNA sequencing for zebrafish early development", "General Sample for zebrafish", "zebrafish early development", null, "breed:wild type zebrafish", null, null, null, null, null, null, null, null, "6 somite of zebrafish development", "6 somite stage", "1", "Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels  and small RNAs were isolated and purified. Subsequently  small RNAs were ligated with both a 5\u2019 adapter and 3\u2019 adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that  the reverse transcribed product  cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec  followed by 15 cycles consisting of 10 sec at 98 oC  15 sec at 72 oC  and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels  the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP028862", null, null, "s6-somite.fq", "fastq", 1023786106.0, 20893594.0, "6 somite", "0:49", "A:231966134;C:225595480;G:271618141;T:294536757;N:69594", 49, null, null, null, 231966134, 225595480, 271618141, 294536757, 69594, "SRX336208", "SRS470740", "SRA098041", "Huazhong University of Science and Technology|cuckoo", "Huazhong University of Science and Technology", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 49, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-07-22", "Segmentation", "Embryo", "Embryo Imprecise", "All anatomical structures"], [37125, "SRR953532", "SRX336173", "SRS470740", "SRP028862", "PRJNA215266", "Danio rerio Transcriptome or Gene expression", "PRJNA215266", "Other", "During early vertebrate development  various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.", null, null, "small RNA sequencing for zebrafish early development", "General Sample for zebrafish", "zebrafish early development", null, "breed:wild type zebrafish", null, null, null, null, null, null, null, null, "5.3hpf of zebrafish development", "5.3hpf stage", "1", "Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels  and small RNAs were isolated and purified. Subsequently  small RNAs were ligated with both a 5\u2019 adapter and 3\u2019 adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that  the reverse transcribed product  cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec  followed by 15 cycles consisting of 10 sec at 98 oC  15 sec at 72 oC  and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels  the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP028862", null, null, "s53-h.fq", "fastq", 1007880412.0, 20568988.0, "5.3hpf", "0:49", "A:226128850;C:222011747;G:262126135;T:297544238;N:69442", 49, null, null, null, 226128850, 222011747, 262126135, 297544238, 69442, "SRX336173", "SRS470740", "SRA098041", "Huazhong University of Science and Technology|cuckoo", "Huazhong University of Science and Technology", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 49, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-07-22", "Gastrula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [37126, "SRR953531", "SRX336172", "SRS470740", "SRP028862", "PRJNA215266", "Danio rerio Transcriptome or Gene expression", "PRJNA215266", "Other", "During early vertebrate development  various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.", null, null, "small RNA sequencing for zebrafish early development", "General Sample for zebrafish", "zebrafish early development", null, "breed:wild type zebrafish", null, null, null, null, null, null, null, null, "oblong of zebrafish development", "oblong stage", "1", "Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels  and small RNAs were isolated and purified. Subsequently  small RNAs were ligated with both a 5\u2019 adapter and 3\u2019 adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that  the reverse transcribed product  cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec  followed by 15 cycles consisting of 10 sec at 98 oC  15 sec at 72 oC  and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels  the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP028862", null, null, "oblong.fq", "fastq", 1016928850.0, 20753650.0, "oblong", "0:49", "A:224798674;C:224915257;G:271761873;T:295384794;N:68252", 49, null, null, null, 224798674, 224915257, 271761873, 295384794, 68252, "SRX336172", "SRS470740", "SRA098041", "Huazhong University of Science and Technology|cuckoo", "Huazhong University of Science and Technology", 1, 1e-05, null, 0.0, null, 0.99997, null, 1.0, null, 49, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-07-22", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [37127, "SRR953530", "SRX336171", "SRS470740", "SRP028862", "PRJNA215266", "Danio rerio Transcriptome or Gene expression", "PRJNA215266", "Other", "During early vertebrate development  various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.", null, null, "small RNA sequencing for zebrafish early development", "General Sample for zebrafish", "zebrafish early development", null, "breed:wild type zebrafish", null, null, null, null, null, null, null, null, "512 cell of zebrafish development", "512 cell stage", "1", "Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels  and small RNAs were isolated and purified. Subsequently  small RNAs were ligated with both a 5\u2019 adapter and 3\u2019 adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that  the reverse transcribed product  cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec  followed by 15 cycles consisting of 10 sec at 98 oC  15 sec at 72 oC  and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels  the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP028862", null, null, "s512-cell.fq", "fastq", 991550035.0, 20235715.0, "512 cell", "0:49", "A:213493042;C:219665976;G:263488396;T:294834622;N:67999", 49, null, null, null, 213493042, 219665976, 263488396, 294834622, 67999, "SRX336171", "SRS470740", "SRA098041", "Huazhong University of Science and Technology|cuckoo", "Huazhong University of Science and Technology", 1, 4e-05, null, 1e-05, null, 0.99993, null, 1.0, null, 49, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-07-22", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [37128, "SRR953522", "SRX336167", "SRS470740", "SRP028862", "PRJNA215266", "Danio rerio Transcriptome or Gene expression", "PRJNA215266", "Other", "During early vertebrate development  various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.", null, null, "small RNA sequencing for zebrafish early development", "General Sample for zebrafish", "zebrafish early development", null, "breed:wild type zebrafish", null, null, null, null, null, null, null, null, "16 cell of zebrafish development", "16 cell stage", "1", "Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels  and small RNAs were isolated and purified. Subsequently  small RNAs were ligated with both a 5\u2019 adapter and 3\u2019 adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that  the reverse transcribed product  cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec  followed by 15 cycles consisting of 10 sec at 98 oC  15 sec at 72 oC  and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels  the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP028862", null, null, "s16-cell.fq", "fastq", 857702468.0, 17504132.0, "16 cell stage", "0:49", "A:188518867;C:188172489;G:222316155;T:258636924;N:58033", 49, null, null, null, 188518867, 188172489, 222316155, 258636924, 58033, "SRX336167", "SRS470740", "SRA098041", "Huazhong University of Science and Technology|cuckoo", "Huazhong University of Science and Technology", 1, 3e-05, null, 1e-05, null, 0.99993, null, 1.0, null, 49, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-07-22", "Cleavage", "Embryo", "Embryo Imprecise", "All anatomical structures"], [37129, "SRR953087", "SRX335692", "SRS470740", "SRP028862", "PRJNA215266", "Danio rerio Transcriptome or Gene expression", "PRJNA215266", "Other", "During early vertebrate development  various small non coding RNAs sRNAs such as MicroRNAs miRNAs and Piwi interacting RNAs piRNAs are dynamically expressed for orchestrating the maternal to zygotic transition MZT. Systematic analysis of expression profiles of zebrafish small RNAome will be greatly helpful for understanding the sRNA regulation during embryonic development.", null, null, "small RNA sequencing for zebrafish early development", "General Sample for zebrafish", "zebrafish early development", null, "breed:wild type zebrafish", null, null, null, null, null, null, null, null, "1 cell of zebrafish development", "1 cell stage", "1", "Total RNA from embryos was isolated using Trizol reagent Invitrogen. RNAs were fractioned on 15% denaturing polyacrylamide gels  and small RNAs were isolated and purified. Subsequently  small RNAs were ligated with both a 5\u2019 adapter and 3\u2019 adapter for reverse transcription using SuperscriptTM II reverse transcription kit Invitrogen following the manufacturer's instructions at 42 oC for 1 h and 70 oC for 15 min. post that  the reverse transcribed product  cDNA was amplified by the following PCR program: a 15 cycle reaction at 98 oC for 30 sec  followed by 15 cycles consisting of 10 sec at 98 oC  15 sec at 72 oC  and then 10 min at 72 oC. post obtaining a 92bp DNA band on 6% denaturing PAGE gels  the PCR products were enriched by ethanol precipitation and purified using Spin X filter columns Fisher.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>49</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP028862", null, null, null, null, 1002077048.0, 20450552.0, "1 cell stage", "0:49", "A:210178307;C:226566574;G:255003953;T:310259058;N:69156", 49, null, null, null, 210178307, 226566574, 255003953, 310259058, 69156, "SRX335692", "SRS470740", "SRA098041", "Huazhong University of Science and Technology|cuckoo", "Huazhong University of Science and Technology", 1, 0.0001, null, 3e-05, null, 0.99975, null, 0.76923, null, 49, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2015-07-22", "Undetermined", "Embryo", "Embryo Imprecise", "All anatomical structures"], [37905, "SRR1138230", "SRX445323", "SRS540474", "SRP035565", "PRJNA236050", "Systematic Transcriptome Analysis of Zebrafish Model of Diamond Blackfan Anemia from RPS24 Deficiency miRNA Seq", "GSE54259", "Transcriptome Analysis", "In this study  we found RPS24 is required for both the primitive hematopoiesis and definitive hematopoiesis process partly mediated by P53 pathway. With the RNA seq and miRNA seq technique  several deregulated genes and miRNAs were found to be related with hematopoiesis  vascular development and apoptosis process in RPS24 deficient zebrafish. Meanwhile  a comprehensive regulatory network was firstly constructed to indentify the mechanisms of key miRNAs and gene pathways in this Model of Diamond Blackfan Anemia. Interestingly  we found that the central nodes genes in the network were almost all targeted by significantly deregulated miRNAs  with partial verification from previous studies  revealing that our network based approach is promising for the identification of new and important miRNAs in DBA. The present study provided comprehensive potential pathogenic genes and miRNAs data that are associated with RPS24 deficient zebrafish embryos as a model of DBA  which should provide a valuable resource for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases. Overall design: Determine the differences of miRNome between RPS24 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases", "parent bioproject:PRJNA236073", "pubmed:25189322;pubmed:26961822", null, "RPS24 MO miRNA Seq", "GSM1311219", null, "tissue:embryo|genotype:RPS24 morpholino knockdown|developmental stage:embryo 48hpf", "RPS24 MO miRNA Seq", "FASTX Toolkit clipper was used to remove sequencing adapters. The .fastq file was converted to a tab delimited file which held only the unique sequence read and its corresponding number of copies. The files were uploaded to DSAP http://dsap.cgu.edu.tw/index.htm for clustering of tags  classification of non coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively. The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP. Genome build: Zv9", "embryo", "Zebrafish embryos at the one cell stage were injected with the MOs using an Microinjector WPI SYS PV830. Based on initial injection trials  2 5 ng MO and control MO was chosen as the optimal concentration.", "Immediately post harvesting  40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at  80\u00b0C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer\u2019s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer\u2019s instructions.", "Zebrafish embryos were kept in a 28.5\u2103 incubator to 48hpf", "genotype:RPS24 morpholino knockdown|developmental stage:embryo 48hpf", "GSM1311219", "GSM1311219: RPS24 MO miRNA Seq; Danio rerio; RNA Seq", "GSM1311219", null, "1", "Immediately post harvesting  40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at  80\u00b0C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer\u2019s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer\u2019s instructions.", "GEO Accession:GSM1311219", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP035565", null, null, "s_7_IDX18_1.fq", "fastq", 883114731.0, 10902651.0, "GSM1311219 r1", "0:81", "A:189355667;C:238092214;G:225845644;T:229789867;N:31339", 81, null, null, null, 189355667, 238092214, 225845644, 229789867, 31339, "SRX445323", "SRS540474", "SRA128456", "GEO", "Beijing Institute of Genomics", 1, 4e-05, null, 0.0, null, 0.99991, null, 1.0, null, 81, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2014-01-21", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [37906, "SRR1138229", "SRX445322", "SRS540473", "SRP035565", "PRJNA236050", "Systematic Transcriptome Analysis of Zebrafish Model of Diamond Blackfan Anemia from RPS24 Deficiency miRNA Seq", "GSE54259", "Transcriptome Analysis", "In this study  we found RPS24 is required for both the primitive hematopoiesis and definitive hematopoiesis process partly mediated by P53 pathway. With the RNA seq and miRNA seq technique  several deregulated genes and miRNAs were found to be related with hematopoiesis  vascular development and apoptosis process in RPS24 deficient zebrafish. Meanwhile  a comprehensive regulatory network was firstly constructed to indentify the mechanisms of key miRNAs and gene pathways in this Model of Diamond Blackfan Anemia. Interestingly  we found that the central nodes genes in the network were almost all targeted by significantly deregulated miRNAs  with partial verification from previous studies  revealing that our network based approach is promising for the identification of new and important miRNAs in DBA. The present study provided comprehensive potential pathogenic genes and miRNAs data that are associated with RPS24 deficient zebrafish embryos as a model of DBA  which should provide a valuable resource for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases. Overall design: Determine the differences of miRNome between RPS24 deficient and MO control zebrafish embryos for understanding the complex molecular pathogenesis of mutant RPS24 mediated human diseases", "parent bioproject:PRJNA236073", "pubmed:25189322;pubmed:26961822", null, "morpholino control miRNA Seq", "GSM1311218", null, "tissue:embryo|genotype:control morpholino|developmental stage:embryo 48hpf", "morpholino control miRNA Seq", "FASTX Toolkit clipper was used to remove sequencing adapters. The .fastq file was converted to a tab delimited file which held only the unique sequence read and its corresponding number of copies. The files were uploaded to DSAP http://dsap.cgu.edu.tw/index.htm for clustering of tags  classification of non coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively. The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP. Genome build: Zv9", "embryo", "Zebrafish embryos at the one cell stage were injected with the MOs using an Microinjector WPI SYS PV830. Based on initial injection trials  2 5 ng MO and control MO was chosen as the optimal concentration.", "Immediately post harvesting  40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at  80\u00b0C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer\u2019s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer\u2019s instructions.", "Zebrafish embryos were kept in a 28.5\u2103 incubator to 48hpf", "genotype:control morpholino|developmental stage:embryo 48hpf", "GSM1311218", "GSM1311218: morpholino control miRNA Seq; Danio rerio; RNA Seq", "GSM1311218", null, "1", "Immediately post harvesting  40 50 pooled embryos at 48 hpf from different experiment replicates were snap frozen in liquid nitrogen and stored at  80\u00b0C. Total RNA was extracted from the pooled embryos using TRIzol Invitrogen according to the manufacturer\u2019s instructions. small RNA libraries were constructed using the Illumina miRNA Seq library preparation kit according to the manufacturer\u2019s instructions.", "GEO Accession:GSM1311218", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP035565", null, null, "s_8_IDX21_1.fq", "fastq", 308681847.0, 3810887.0, "GSM1311218 r1", "0:81", "A:63686404;C:75263287;G:80056961;T:89650625;N:24570", 81, null, null, null, 63686404, 75263287, 80056961, 89650625, 24570, "SRX445322", "SRS540473", "SRA128456", "GEO", "Beijing Institute of Genomics", 1, 8e-05, null, 2e-05, null, 0.99991, null, 0.42857, null, 81, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2014-01-21", "Hatching", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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. 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 kiss1KO Replicate2", "zebrafish AO149 01T0004", null, "strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:kiss1 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 kiss1KO larvae 2", "RNA Seq for  zebrafish  kiss1KO  larvae 2", "RNA Seq   zebrafish  kiss1KO  larvae 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP437283", null, null, "Unknown_AO149-01T0004_good_1.fq.gz Unknown_AO149-01T0004_good_2.fq.gz", "fastq fastq", 5814495346.0, 19499621.0, "Unknown AO149 01T0004 good 1.fq.gz", "0:149.09 1:149.09", "A:1528388873;C:1369910846;G:1386794007;T:1529368087;N:33533", 149, 149, null, null, 1528388873, 1369910846, 1386794007, 1529368087, 33533, "SRX20302023", "SRS17627880", "SRA1636880", "Soochow University|Medical College", "Soochow University", 2, 0.94765, 0.94711, 0.07972, 0.07979, 0.65283, 0.65397, 0.48362, 0.48203, 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"], [75419, "SRR24517734", "SRX20302022", "SRS17627877", "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 kiss1KO Replicate1", "zebrafish AO149 01T0003", null, "strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:kiss1 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 kiss1KO larvae 1", "RNA Seq for  zebrafish kiss1KO larvae 1", "RNA Seq   zebrafish kiss1KO larvae 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP437283", null, null, "Unknown_AO149-01T0003_good_1.fq.gz Unknown_AO149-01T0003_good_2.fq.gz", "fastq fastq", 6174484352.0, 20748774.0, "Unknown AO149 01T0003 good 1.fq.gz", "0:148.79 1:148.79", "A:1629263285;C:1446858897;G:1467609266;T:1630717493;N:35411", 148, 148, null, null, 1629263285, 1446858897, 1467609266, 1630717493, 35411, "SRX20302022", "SRS17627877", "SRA1636880", "Soochow University|Medical College", "Soochow University", 2, 0.94831, 0.94853, 0.07898, 0.07866, 0.65295, 0.65419, 0.47605, 0.47682, 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"], [75420, "SRR24517735", "SRX20302021", "SRS17627878", "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 wt Replicate2", "zebrafish AO149 01T0002", null, "strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:WT|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 WT larvae 2", "RNA Seq  for zebrafish WT  larvae 2", "RNA Seq   zebrafish WT  larvae 2", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP437283", null, null, "Unknown_AO149-01T0002_good_1.fq.gz Unknown_AO149-01T0002_good_2.fq.gz", "fastq fastq", 6059983436.0, 20361363.0, "Unknown AO149 01T0002 good 1.fq.gz", "0:148.81 1:148.81", "A:1608075382;C:1408291949;G:1433236990;T:1610344312;N:34803", 148, 148, null, null, 1608075382, 1408291949, 1433236990, 1610344312, 34803, "SRX20302021", "SRS17627878", "SRA1636880", "Soochow University|Medical College", "Soochow University", 2, 0.9529, 0.95334, 0.07296, 0.07315, 0.65435, 0.65247, 0.49743, 0.47334, 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"], [75421, "SRR24517736", "SRX20302020", "SRS17627876", "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 wt Replicate1", "zebrafish AO149 01T0001", null, "strain:AB|age:5dpf|dev stage:larvae|sex:not determined|tissue:whole organism|collection date:2020|genotype:WT|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 WT larvae 1", "RNA Seq for zebrafish WT larvae 1", "RNA Seq   zebrafish WT larvae 1", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "PAIRED", "ILLUMINA", "HiSeq X Five", null, "SRP437283", null, null, "Unknown_AO149-01T0001_good_1.fq.gz Unknown_AO149-01T0001_good_2.fq.gz", "fastq fastq", 6809997812.0, 22853255.0, "Unknown AO149 01T0001 good 1.fq.gz", "0:148.99 1:148.99", 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