rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
32541,SRR29303120,SRX24820197,SRS21534299,SRP512097,PRJNA1120592,Light induce Zebrafish larvae,PRJNA1120592,Other,Light induce Zebrafish larvae  miRNA,,,,,L6H 1 miRNA,,breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 10|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA seq of zebrafish larvae,L6H 1,L6H 1,miRNA  seq,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP512097,,,L6H_1.fq.gz,fastq,619966455.0,12156205.0,L6H 1.fq.gz,0:51,A:143411079;C:162001488;G:168382605;T:146007422;N:163861,51,,,,143411079,162001488,168382605,146007422,163861,SRX24820197,SRS21534299,SRA1890590,Lanzhou University|College of Life Science,Lanzhou University,1,0.01303,,0.00337,,0.99472,,0.5628,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-06-06,Larval,Larval,Trunk,Surface Structure
32542,SRR29303121,SRX24820196,SRS21534298,SRP512097,PRJNA1120592,Light induce Zebrafish larvae,PRJNA1120592,Other,Light induce Zebrafish larvae  miRNA,,,,,L3H 3 miRNA,,breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 09|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA seq of zebrafish larvae,L3H 3,L3H 3,miRNA  seq,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP512097,,,L3H_3.fq.gz,fastq,738125703.0,14473053.0,L3H 3.fq.gz,0:51,A:176614297;C:190760467;G:197157923;T:173400138;N:192878,51,,,,176614297,190760467,197157923,173400138,192878,SRX24820196,SRS21534298,SRA1890590,Lanzhou University|College of Life Science,Lanzhou University,1,0.01163,,0.00356,,0.99379,,0.55469,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-06-06,Larval,Larval,Trunk,Surface Structure
32543,SRR29303122,SRX24820195,SRS21534297,SRP512097,PRJNA1120592,Light induce Zebrafish larvae,PRJNA1120592,Other,Light induce Zebrafish larvae  miRNA,,,,,L3H 2 miRNA,,breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 08|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA seq of zebrafish larvae,L3H 2,L3H 2,miRNA  seq,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP512097,,,L3H_2.fq.gz,fastq,489154821.0,9591271.0,L3H 2.fq.gz,0:51,A:109695797;C:132121151;G:127787221;T:119539033;N:11619,51,,,,109695797,132121151,127787221,119539033,11619,SRX24820195,SRS21534297,SRA1890590,Lanzhou University|College of Life Science,Lanzhou University,1,0.05359,,0.01132,,0.98924,,0.55364,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-06-06,Larval,Larval,Trunk,Surface Structure
32544,SRR29303123,SRX24820194,SRS21534296,SRP512097,PRJNA1120592,Light induce Zebrafish larvae,PRJNA1120592,Other,Light induce Zebrafish larvae  miRNA,,,,,L3H 1 miRNA,,breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 07|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA seq of zebrafish larvae,L3H 1,L3H 1,miRNA  seq,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP512097,,,L3H_1.fq.gz,fastq,551502015.0,10813765.0,L3H 1.fq.gz,0:51,A:130437158;C:141969110;G:146479841;T:132605147;N:10759,51,,,,130437158,141969110,146479841,132605147,10759,SRX24820194,SRS21534296,SRA1890590,Lanzhou University|College of Life Science,Lanzhou University,1,0.13403,,0.01834,,0.98735,,0.54849,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-06-06,Larval,Larval,Trunk,Surface Structure
32545,SRR29303124,SRX24820193,SRS21534295,SRP512097,PRJNA1120592,Light induce Zebrafish larvae,PRJNA1120592,Other,Light induce Zebrafish larvae  miRNA,,,,,L1H 3 miRNA,,breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 06|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA seq of zebrafish larvae,L1H 3,L1H 3,miRNA  seq,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP512097,,,L1H_3.fq.gz,fastq,524533827.0,10284977.0,L1H 3.fq.gz,0:51,A:118598837;C:136729611;G:142993590;T:126201873;N:9916,51,,,,118598837,136729611,142993590,126201873,9916,SRX24820193,SRS21534295,SRA1890590,Lanzhou University|College of Life Science,Lanzhou University,1,0.00829,,0.00187,,0.99472,,0.54701,,51,,T,,under 1.2% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-06-06,Larval,Larval,Trunk,Surface Structure
32546,SRR29303125,SRX24820192,SRS21534294,SRP512097,PRJNA1120592,Light induce Zebrafish larvae,PRJNA1120592,Other,Light induce Zebrafish larvae  miRNA,,,,,L1H 2 miRNA,,breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 05|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA seq of zebrafish larvae,L1H 2,L1H 2,miRNA  seq,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP512097,,,L1H_2.fq.gz,fastq,541697163.0,10621513.0,L1H 2.fq.gz,0:51,A:126751483;C:135818134;G:141122995;T:137953543;N:51008,51,,,,126751483,135818134,141122995,137953543,51008,SRX24820192,SRS21534294,SRA1890590,Lanzhou University|College of Life Science,Lanzhou University,1,0.33438,,0.08101,,0.98238,,0.53337,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-06-06,Larval,Larval,Trunk,Surface Structure
32547,SRR29303126,SRX24820191,SRS21534293,SRP512097,PRJNA1120592,Light induce Zebrafish larvae,PRJNA1120592,Other,Light induce Zebrafish larvae  miRNA,,,,,L1H 1 miRNA,,breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 04|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA seq of zebrafish larvae,L1H 1,L1H 1,miRNA  seq,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP512097,,,L1H_1.fq.gz,fastq,930096282.0,18237182.0,L1H 1.fq.gz,0:51,A:212568445;C:243497911;G:260145458;T:213851032;N:33436,51,,,,212568445,243497911,260145458,213851032,33436,SRX24820191,SRS21534293,SRA1890590,Lanzhou University|College of Life Science,Lanzhou University,1,0.64143,,0.02683,,0.98683,,0.5342,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-06-06,Larval,Larval,Trunk,Surface Structure
32548,SRR29303127,SRX24820190,SRS21534292,SRP512097,PRJNA1120592,Light induce Zebrafish larvae,PRJNA1120592,Other,Light induce Zebrafish larvae  miRNA,,,,,DD 3 miRNA,,breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 03|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA seq of zebrafish larvae,DD 3,DD 3,miRNA  seq,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP512097,,,DD_3.fq.gz,fastq,667459389.0,13087439.0,DD 3.fq.gz,0:51,A:157267065;C:168909886;G:178336724;T:162865168;N:80546,51,,,,157267065,168909886,178336724,162865168,80546,SRX24820190,SRS21534292,SRA1890590,Lanzhou University|College of Life Science,Lanzhou University,1,0.19375,,0.03528,,0.98827,,0.55124,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-06-06,Larval,Larval,Trunk,Surface Structure
32549,SRR29303128,SRX24820189,SRS21534291,SRP512097,PRJNA1120592,Light induce Zebrafish larvae,PRJNA1120592,Other,Light induce Zebrafish larvae  miRNA,,,,,L6H 3 miRNA,,breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 12|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA seq of zebrafish larvae,L6H 3,L6H 3,miRNA  seq,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP512097,,,L6H_3.fq.gz,fastq,551181072.0,10807472.0,L6H 3.fq.gz,0:51,A:126813056;C:141881980;G:147676363;T:134665008;N:144665,51,,,,126813056,141881980,147676363,134665008,144665,SRX24820189,SRS21534291,SRA1890590,Lanzhou University|College of Life Science,Lanzhou University,1,0.09301,,0.01507,,0.99042,,0.54323,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-06-06,Larval,Larval,Trunk,Surface Structure
32550,SRR29303129,SRX24820188,SRS21534290,SRP512097,PRJNA1120592,Light induce Zebrafish larvae,PRJNA1120592,Other,Light induce Zebrafish larvae  miRNA,,,,,L6H 2 miRNA,,breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 11|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA seq of zebrafish larvae,L6H 2,L6H 2,miRNA  seq,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP512097,,,L6H_2.fq.gz,fastq,571762632.0,11211032.0,L6H 2.fq.gz,0:51,A:138521192;C:148068464;G:150615597;T:134408189;N:149190,51,,,,138521192,148068464,150615597,134408189,149190,SRX24820188,SRS21534290,SRA1890590,Lanzhou University|College of Life Science,Lanzhou University,1,0.01523,,0.00336,,0.9933,,0.57685,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-06-06,Larval,Larval,Trunk,Surface Structure
32551,SRR29303130,SRX24820187,SRS21534289,SRP512097,PRJNA1120592,Light induce Zebrafish larvae,PRJNA1120592,Other,Light induce Zebrafish larvae  miRNA,,,,,DD 2 miRNA,,breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 02|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA seq of zebrafish larvae,DD 2,DD 2,miRNA  seq,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP512097,,,DD_2.fq.gz,fastq,706940937.0,13861587.0,DD 2.fq.gz,0:51,A:162899595;C:189209828;G:187422113;T:167222837;N:186564,51,,,,162899595,189209828,187422113,167222837,186564,SRX24820187,SRS21534289,SRA1890590,Lanzhou University|College of Life Science,Lanzhou University,1,0.02266,,0.00566,,0.99334,,0.56959,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-06-06,Larval,Larval,Trunk,Surface Structure
32552,SRR29303131,SRX24820186,SRS21534288,SRP512097,PRJNA1120592,Light induce Zebrafish larvae,PRJNA1120592,Other,Light induce Zebrafish larvae  miRNA,,,,,DD 1 miRNA,,breed:zebrafish|cultivar:not applicable|ecotype:AB|age:5 dpf|dev stage:larvae|collection date:2020 10 01|geo loc name:China: Lanzhou|sex:not determined|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA seq of zebrafish larvae,DD 1,DD 1,miRNA  seq,,,miRNA-Seq,TRANSCRIPTOMIC,RANDOM PCR,SINGLE,ILLUMINA,Illumina HiSeq 3000,,SRP512097,,,DD_1.fq.gz,fastq,540332862.0,10594762.0,DD 1.fq.gz,0:51,A:127336994;C:143901414;G:142437491;T:126515166;N:141797,51,,,,127336994,143901414,142437491,126515166,141797,SRX24820186,SRS21534288,SRA1890590,Lanzhou University|College of Life Science,Lanzhou University,1,0.01404,,0.00313,,0.99484,,0.56573,,51,,B,,usable mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,China,2024-06-06,Larval,Larval,Trunk,Surface Structure
39609,SRR1873571,SRX915251,SRS870223,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,fins,GSM1630515,,source name:adult fins 1 year old|strain/background:AB|genotype/variation:wild type|tissue:fins|developmental stage:adult|age:1 year,fins,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,adult fins 1 year old,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:fins|developmental stage:adult|age:1 year,GSM1630515,GSM1630515: fins; Danio rerio; miRNA Seq,GSM1630515,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630515,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,113161.0,2108.0,GSM1630515 r1,0:4 1:49.68,A:30303;C:30710;G:27210;T:24785;N:153,4,49,,,30303,30710,27210,24785,153,SRX915251,SRS870223,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,50,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Adult,Adult,Fin,Surface Structure
39610,SRR1873570,SRX915250,SRS870224,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,skin,GSM1630514,,source name:adult skin 1 year old|strain/background:AB|genotype/variation:wild type|tissue:skin|developmental stage:adult|age:1 year,skin,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,adult skin 1 year old,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:skin|developmental stage:adult|age:1 year,GSM1630514,GSM1630514: skin; Danio rerio; miRNA Seq,GSM1630514,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630514,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,79232.0,1527.0,GSM1630514 r1,0:4 1:47.89,A:20622;C:23508;G:19017;T:15967;N:118,4,47,,,20622,23508,19017,15967,118,SRX915250,SRS870224,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,53,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Adult,Adult,Skin,Surface Structure
39615,SRR1873565,SRX915245,SRS870229,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,adult,GSM1630509,,source name:entire adult|strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:adult|age:1 year,adult,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,entire adult,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:adult|age:1 year,GSM1630509,GSM1630509: adult; Danio rerio; miRNA Seq,GSM1630509,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630509,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,361024.0,6498.0,GSM1630509 r1,0:4 1:51.56,A:104704;C:84406;G:83224;T:87843;N:847,4,51,,,104704,84406,83224,87843,847,SRX915245,SRS870229,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,51,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Adult,Adult,Trunk,Surface Structure
39616,SRR1873564,SRX915244,SRS870230,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,45dpf,GSM1630508,,source name:45 dpf embryos|strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:45dpf,45dpf,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,45 dpf embryos,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:45dpf,GSM1630508,GSM1630508: 45dpf; Danio rerio; miRNA Seq,GSM1630508,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630508,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,123960.0,2248.0,GSM1630508 r1,0:4 1:51.14,A:38130;C:31332;G:30088;T:24223;N:187,4,51,,,38130,31332,30088,24223,187,SRX915244,SRS870230,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,52,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Juvenile,Juvenile,Trunk,Surface Structure
39617,SRR1873563,SRX915243,SRS870231,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,5dpf,GSM1630507,,source name:5 dpf embryos|strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:5dpf,5dpf,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,5 dpf embryos,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:5dpf,GSM1630507,GSM1630507: 5dpf; Danio rerio; miRNA Seq,GSM1630507,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630507,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,168981.0,3060.0,GSM1630507 r1,0:4 1:51.22,A:51895;C:42870;G:40864;T:32741;N:611,4,51,,,51895,42870,40864,32741,611,SRX915243,SRS870231,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,50,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Larval,Larval,Trunk,Surface Structure
39618,SRR1873562,SRX915242,SRS870232,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,96hpf,GSM1630506,,source name:96 hpf embryos|strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:96hpf,96hpf,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,96 hpf embryos,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:96hpf,GSM1630506,GSM1630506: 96hpf; Danio rerio; miRNA Seq,GSM1630506,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630506,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,61235.0,1109.0,GSM1630506 r1,0:4 1:51.22,A:18594;C:15084;G:15091;T:12247;N:219,4,51,,,18594,15084,15091,12247,219,SRX915242,SRS870232,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,52,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Larval,Larval,Trunk,Surface Structure
39619,SRR1873561,SRX915241,SRS870233,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,72hpf,GSM1630505,,source name:72 hpf embryos|strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:72hpf,72hpf,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,72 hpf embryos,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:72hpf,GSM1630505,GSM1630505: 72hpf; Danio rerio; miRNA Seq,GSM1630505,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630505,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,778415.0,14183.0,GSM1630505 r1,0:4 1:50.88,A:231211;C:186354;G:190297;T:169348;N:1205,4,50,,,231211,186354,190297,169348,1205,SRX915241,SRS870233,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,48,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Larval,Larval,Trunk,Surface Structure
39620,SRR1873560,SRX915240,SRS870234,SRP056014,PRJNA277780,Identification of small non coding RNAs in zebrafish,GSE66718,Transcriptome Analysis,MicroRNAs miRNAs are a new class of small RNAs of approximately 22 nucleotides in length that control eukaryotic gene expression by fine tuning mRNA translation. They regulate a wide variety of biological processes  namely developmental timing  cell differentiation  cell proliferation  immune response and infection. For this reason  their identification is essential to understand eukaryotic biology. Their small size  low abundance and high instability complicated early identification; however  cloning/Sanger sequencing and new generation genome sequencing approaches overcame most technical hurdles and are being used for rapid miRNA identification in many eukaryotes. We have applied 454 DNA pyrosequencing technology to miRNA discovery in zebrafish Danio rerio. For this  a series of cDNA libraries were prepared from small non coding RNAs isolated at different embryonic time points and from fully developed organs. Each cDNA library was tagged with specific sequences and was sequenced using the Roche FLX genome sequencer. This approach retrieved 90% of the 192 miRNAs previously identified by cloning/Sanger sequencing and bioinformatics and 25 novel miRNAs were predicted. Overall design: Small RNA libraries were prepared from different zebrafish developmental stages  namely  24 hpf  72 hpf  96 hpf  5 dpf dpf  45 dpf  young adult and from adult brain  eyes  gills  heart  skin and fins.,,pubmed:26694924,,24hpf,GSM1630504,,source name:24 hpf embryos|strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:24hpf,24hpf,Base calling and quality trimming of sequence reads was carried out using the Genome Sequencer FLX software. Raw images were processed to remove background noise and the data was normalized. TAGs and adapter sequences of zebrafish developmental and adult tissues samples were then identified and trimmed and those reads with correct TAGs and adapters > 15 nt were retrieved for downstream analysis using the miRDeep software https://www.mdc berlin.de/8551903/en/. miRDeep aligned the sequences against the zebrafish genome using megaBlast with seed length set at 12  the traditional blast output  and minimum local identity set at 100. The blast output was then parsed for miRDeep uploading and aligned sequences with a maximum of 2 mismatches in the three prime end were retrieved. Reads that matched more than 10 different genome loci were discarded and only those with one or more alignments were kept  and using the remaining alignments as guidelines  the potential precursors were excised from the genome. The secondary structure of putative precursors was predicted using RNAfold and signatures were created by retaining reads that aligned perfectly with those putative precursors to generate the signature format. Finally  miRDeep predicted miRNAs by discarding non plausible Dicer products and scoring plausible ones. To assess seed conservation  plausible Dicer processing sequences were blasted against a local version of mature miRNAs from miRBase 12.0 that lacked zebrafish miRNA sequences. Borderline miRNA candidates were also resolved by determining their relative stability using Randfold. To distinguish between novel and known miRNAs  selected pre miRNAs were blasted against Danio rerio stem loop sequences miRBase and those that did not produce any or produced imperfect alignments were scored as novel miRNAs. Pairs of signatures and structures were used to estimate the number of false positives by randomly permutation  using miRDeep. To overcome the inherent lack of sensitivity of miRDeep  novel transcripts encoding miRNAs predicted by bioinformatics were retrieved from Ensembl 5.2 using BioMart and from literature predictions. These sequences were then used to perform a megaBlast search against our data with seed length set at 12. The transcripts with perfect matches and alignment length larger than 18 nt were kept for further processing. These transcripts were then compared with the mature miRNAs present in miRBase 12.0 and those that produced imperfect alignments or did not produce alignments were considered new miRNAs. Read numbers were normalized as described by Chen and colleagues Genes & Development 2005  19:1288 1293  and a miRNA expression profile  using identical number of reads for each sample  was generated. The number of reads between samples was normalized as indicated below:  Expression Reads = [1000 x NRmiRNAXY]/ TNRmiRNAsY  where NRmiRNAXY is the number of reads of miRNAX X = any miRNA in sample Y  and TNRmiRNAsY is the total number of miRNAs in sample Y. 1000 is an arbitrary number of reads. The data was transformed into log2 scale to build the heat map using the MeV 4.0 software package http://www.tm4.org/mev.html. Genome build: Zv8 Supplementary files format and content: Tab delimited text files include the miRNA IDs  sequences and respective raw counts post data processing for each sample.,24 hpf embryos,,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",Wild type AB zebrafish strain was maintained at 28ºC on a 14 h light/10 h dark cycle.,strain/background:AB|genotype/variation:wild type|tissue:whole body|developmental stage:embryo|age:24hpf,GSM1630504,GSM1630504: 24hpf; Danio rerio; miRNA Seq,GSM1630504,,1,"100 μg of total RNA from each sample was isolated using TRIzol® and small RNAs were enriched by differential precipitation using polyethylene glycol. Total RNAs were fractioned using 12% denaturing PAGE and small RNAs of 15 30 nt were gel isolated using Gel Filtration cartridges from Edge Biosystems. For cDNA synthesis  the small RNA molecules previously isolated were first ligated to a three prime adapter AMP five primep five primep/CTGTAGGCACCATCAATdi deoxyC  three prime in absence of ATP and gel excised in the range of 35 and 50 nt. A second ligation was performed with the five prime adapter ""Nelson's linker"" five primeATCGTrArGrGrCrArCrCrUrGrArArA three prime  for 1 hour at 37°C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript™ III reverse transcriptase Invitrogen. RNase H treated cDNA was PCR amplified with adapter specific primers. Each sample contained a specific TAG constituted by 3 nucleotides  as detailed next. 24hpf   ATC; 72hpf   ACT; 96hpf   CAG; 5dpf   ATG; 45dpf   CCG; entire adult   GTA; brain   CGG; Heart   CTG; Eyes   GCT; fins   GTT; skin   TAC; gills   TCC. PCR products were then run on 10% denaturing PAGE containing 7 M urea and the corresponding band 100 nt was eluted from the gel with Probe Elution Buffer from Ambion  at 37°C overnight. These products were used for the emulsion PCR. Parallel DNA pyrosequencing was performed using the Genome Sequencer FLX Roche  following established protocols for DNA library sequencing.",GEO Accession:GSM1630504,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,LS454,454 GS FLX,,SRP056014,,,,,6831.0,129.0,GSM1630504 r1,0:4 1:48.95,A:1947;C:1747;G:1688;T:1424;N:25,4,48,,,1947,1747,1688,1424,25,SRX915240,SRS870234,SRA246117,GEO,University of Aveiro,1,0.0,,0.0,,1.0,,,,46,,T,,under 1.2% mapping rate,legacy,early,3prime,size_fractionation,unknown,bulk,other_seq,454,,Portugal,2015-03-09,Pharyngula,Embryo,Trunk,Surface Structure
41421,SRR4423115,SRX2245299,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,94 3,94 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0094BC03smallZF.fastq,fastq,697814234.0,14408051.0,maleRID0094BC03smallZF.fastq,0:48.43,A:165337411;C:177790468;G:184204311;T:170482044;N:0,48,,,,165337411,177790468,184204311,170482044,0,SRX2245299,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.70426,,0.16215,,0.91027,,0.5459,,120,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
41425,SRR4423111,SRX2245295,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,88 3,88 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0088BC03smallZF.fastq,fastq,523776538.0,11118832.0,maleRID0088BC03smallZF.fastq,0:47.11,A:123827431;C:133478804;G:138882662;T:127587641;N:0,47,,,,123827431,133478804,138882662,127587641,0,SRX2245295,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.69556,,0.16368,,0.9093,,0.54838,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
41427,SRR4423109,SRX2245293,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,93 3,93 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0093BC03smallZF.fastq,fastq,692750598.0,14286031.0,maleRID0093BC03smallZF.fastq,0:48.49,A:164412063;C:176380331;G:182539801;T:169418403;N:0,48,,,,164412063,176380331,182539801,169418403,0,SRX2245293,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.70738,,0.16645,,0.90948,,0.55306,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
71643,SRR21869762,SRX17856938,SRS15377982,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,BHEE H 3,,replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 15|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221124,AT20221124,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,BHEE_H_3.fq.gz,fastq,533428889.0,23211223.0,BHEE H 3.fq.gz,0:22.98,A:120057830;C:104713991;G:142506271;T:166150296;N:501,22,,,,120057830,104713991,142506271,166150296,501,SRX17856938,SRS15377982,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.79272,,0.10596,,0.92431,,0.52918,,22,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71644,SRR21869763,SRX17856937,SRS15377981,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,BHEE H 2,,replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 14|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221123,AT20221123,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,BHEE_H_2.fq.gz,fastq,542237520.0,23757627.0,BHEE H 2.fq.gz,0:22.82,A:118608004;C:107602147;G:146341292;T:169685803;N:274,22,,,,118608004,107602147,146341292,169685803,274,SRX17856937,SRS15377981,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.78829,,0.10064,,0.91346,,0.52625,,22,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71645,SRR21869764,SRX17856936,SRS15377980,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,BHEE H 1,,replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 13|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221122,AT20221122,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,BHEE_H_1.fq.gz,fastq,553437966.0,24068768.0,BHEE H 1.fq.gz,0:22.99,A:123764056;C:109954264;G:151884637;T:167834745;N:264,22,,,,123764056,109954264,151884637,167834745,264,SRX17856936,SRS15377980,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.70849,,0.09465,,0.91768,,0.52194,,22,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71646,SRR21869765,SRX17856935,SRS15377979,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,BHEE L 3,,replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 12|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221121,AT20221121,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,BHEE_L_3.fq.gz,fastq,534633614.0,23823089.0,BHEE L 3.fq.gz,0:22.44,A:117363754;C:102332510;G:134833529;T:180103711;N:110,22,,,,117363754,102332510,134833529,180103711,110,SRX17856935,SRS15377979,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.91988,,0.08325,,0.94073,,0.53253,,23,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71647,SRR21869766,SRX17856934,SRS15377978,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,BHEE L 2,,replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 11|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221120,AT20221120,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,BHEE_L_2.fq.gz,fastq,544854900.0,24226737.0,BHEE L 2.fq.gz,0:22.49,A:119782823;C:104902871;G:136756907;T:183412172;N:127,22,,,,119782823,104902871,136756907,183412172,127,SRX17856934,SRS15377978,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.93474,,0.08179,,0.9345,,0.52916,,22,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71648,SRR21869767,SRX17856933,SRS15377990,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,BHEE L 1,,replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 10|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221119,AT20221119,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,BHEE_L_1.fq.gz,fastq,536871966.0,23768969.0,BHEE L 1.fq.gz,0:22.59,A:117321330;C:102381550;G:133641788;T:183527144;N:154,22,,,,117321330,102381550,133641788,183527144,154,SRX17856933,SRS15377990,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.94042,,0.08986,,0.93141,,0.51821,,22,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71649,SRR21869768,SRX17856932,SRS15377989,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,TBBPA H 3,,replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 9|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221118,AT20221118,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,TBBPA_H_3.fq.gz,fastq,528430937.0,23464221.0,TBBPA H 3.fq.gz,0:22.52,A:115261465;C:101477007;G:136961367;T:174730904;N:194,22,,,,115261465,101477007,136961367,174730904,194,SRX17856932,SRS15377989,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.89616,,0.09929,,0.93042,,0.5004,,22,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71650,SRR21869769,SRX17856931,SRS15377988,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,TBBPA H 2,,replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 8|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221117,AT20221117,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,TBBPA_H_2.fq.gz,fastq,523343500.0,22888420.0,TBBPA H 2.fq.gz,0:22.86,A:114272050;C:101352294;G:133914155;T:173804699;N:302,22,,,,114272050,101352294,133914155,173804699,302,SRX17856931,SRS15377988,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.90842,,0.10759,,0.92088,,0.53284,,20,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71651,SRR21869770,SRX17856930,SRS15377987,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,TBBPA H 1,,replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 7|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221116,AT20221116,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,TBBPA_H_1.fq.gz,fastq,538481195.0,23517366.0,TBBPA H 1.fq.gz,0:22.90,A:117132485;C:106262580;G:143962997;T:171122739;N:394,22,,,,117132485,106262580,143962997,171122739,394,SRX17856930,SRS15377987,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.83673,,0.10787,,0.91238,,0.53365,,21,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71652,SRR21869771,SRX17856929,SRS15377986,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,TBBPA L 3,,replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 6|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221115,AT20221115,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,TBBPA_L_3.fq.gz,fastq,536529124.0,23817957.0,TBBPA L 3.fq.gz,0:22.53,A:115664153;C:104457844;G:136444705;T:179962303;N:119,22,,,,115664153,104457844,136444705,179962303,119,SRX17856929,SRS15377986,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.86178,,0.09041,,0.93624,,0.4992,,22,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71654,SRR21869773,SRX17856927,SRS15377985,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,TBBPA L 2,,replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 5|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221114,AT20221114,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,TBBPA_L_2.fq.gz,fastq,525712427.0,23458446.0,TBBPA L 2.fq.gz,0:22.41,A:115172158;C:103930973;G:133832634;T:172776555;N:107,22,,,,115172158,103930973,133832634,172776555,107,SRX17856927,SRS15377985,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.87223,,0.08526,,0.93845,,0.54116,,22,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71655,SRR21869774,SRX17856926,SRS15377984,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,TBBPA L 1,,replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 4|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221113,AT20221113,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,TBBPA_L_1.fq.gz,fastq,527804519.0,23370082.0,TBBPA L 1.fq.gz,0:22.58,A:114266025;C:102477479;G:134403120;T:176657729;N:166,22,,,,114266025,102477479,134403120,176657729,166,SRX17856926,SRS15377984,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.89339,,0.09635,,0.92608,,0.48415,,22,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71656,SRR21869775,SRX17856925,SRS15377983,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,Control 3,,replicate:biological replicate 3|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 3|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221112,AT20221112,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,Control_3.fq.gz,fastq,535579212.0,23899710.0,Control 3.fq.gz,0:22.41,A:117125157;C:106586085;G:133001456;T:178866289;N:225,22,,,,117125157,106586085,133001456,178866289,225,SRX17856925,SRS15377983,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.89094,,0.06851,,0.94807,,0.54835,,23,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71657,SRR21869776,SRX17856924,SRS15377977,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,Control 2,,replicate:biological replicate 2|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 2|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221111,AT20221111,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,Control_2.fq.gz,fastq,528466892.0,23430674.0,Control 2.fq.gz,0:22.55,A:116361274;C:103960709;G:132758802;T:175385846;N:261,22,,,,116361274,103960709,132758802,175385846,261,SRX17856924,SRS15377977,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.89063,,0.07453,,0.94255,,0.54503,,21,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure
71658,SRR21869777,SRX17856923,SRS15377976,SRP402080,PRJNA889683,miRNA mRNA sequencing of zebrafish embryos,PRJNA889683,Other,miRNA Seq and RNA Seq data of zebrafish embryos post exposure to TBBPA and TBBPA BHEE,,,,,Control 1,,replicate:biological replicate 1|strain:AB|isolate:not applicable|breed:wild type|cultivar:not applicable|ecotype:not applicable|age:120 hpf|dev stage:larvae|sex:not applicable|tissue:whole body 1|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of zebrafish larvae,AT20221110,AT20221110,miRNA Seq of zebrafish larvae,,,miRNA-Seq,TRANSCRIPTOMIC,size fractionation,SINGLE,BGISEQ,BGISEQ-500,,SRP402080,,loader:fastq load.py,Control_1.fq.gz,fastq,517484481.0,23046792.0,Control 1.fq.gz,0:22.45,A:114187486;C:101456491;G:129311971;T:172528320;N:213,22,,,,114187486,101456491,129311971,172528320,213,SRX17856923,SRS15377976,SRA1518395,Jiangsu University|School of Environment and Safety Engineering,Jiangsu University,1,0.89811,,0.07533,,0.93198,,0.55322,,22,,B,,usable mapping rate,bgi,bgi,unknown,size_fractionation,unknown,bulk,unknown,unknown,,China,2022-10-12,Larval,Larval,Trunk,Surface Structure