{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_layout = \"SINGLE\", experiment.library_selection = \"size fractionation\" and tissue_curation_coarse = \"Surface Structure\"", "rows": [[36272, "SRR298567", "SRX079845", "SRS212651", "SRP007331", "PRJNA141525", "Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish.", "GSE29418", "Transcriptome Analysis", "RNA libraries from immunoprecipitates of Tdrd1  Ziwi and Zili  total testis RNA  total RNA from 3 wpf wild type and tdrd1 mutant gonads. Overall design: Both size selected and non size selected libraries were made. Sequencing was performed using Illumina platform.", null, "pubmed:21743441", null, "ZiliIPTes", "GSM727524", null, "tissue:RNA obtained from immunoprecipitation with Zili antibody|strain:TL", "ZiliIPTes", "three prime adapter sequences were trimmed and inserts longer than 18 nt were mapped to the D. rerio genome Zv9.", "RNA obtained from immunoprecipitation with Zili antibody", null, "Tissues in IP lysis buffer were sonicated for 2 minutes at 4 oC and centrifuged for 10 minutes at 16000 rpm at 4 oC. Supernatant was used for IP. One IP contains 30 \u00c2\u00b5l Dynabeads Invitrogen  3 or 6 testes  and Zili antibody in a total volume of 500 \u00c2\u00b5l.  RNA was then size selected 18 35 nucleotides from gel. For cDNA synthesis  adaptors were ligated to the three prime and five prime ends of the RNAof the size selected immunoprecipitated fraction. First strand cDNA synthesis was then performed using an oligodT linker primer and M MLVRNase H  reverse transcriptase. cDNA was PCR amplified with adapter specific primers and used in Illumina sequencing.", null, "strain:TL", "GSM727524", "GSM727524: ZiliIPTes", "GSM727524: ZiliIPTes", "GSM727524: ZiliIPTes", "1", null, "GEO Accession:GSM727524", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP007331", null, "read name barcode proc directive:ignore", "ZiliIPTes.fastq", "fastq", 995759064.0, 27659974.0, "GSM727524 1", "0:36", null, 36, null, null, null, null, null, null, null, null, "SRX079845", "SRS212651", "SRA039167", "GEO", "European Research Institute for the Biology of Ageing, University Medical Center Groningen", 1, 0.0537, null, 0.03117, null, 0.95856, null, 0.42091, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2011-05-20", "Undetermined", "Undetermined", "Trunk", "Surface Structure"], [36335, "SRR398322", "SRX115580", "SRS285697", "SRP010291", "PRJNA150927", "miR 221 is required for endothelial tip cell behaviors during vascular development", "GSE35078", "Transcriptome Analysis", "Through deep sequencing and functional screening in zebrafish  we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor.  Furthermore  miR 221 was required for tip cell proliferation and migration  as well as tip cell potential in mosaic blood vessels.  miR 221 knockdown also prevented \u201chyper angiogenesis\u201d defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling.  Finally  miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1.  These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells.", null, "pubmed:22340502", null, "miRNA GFP minus", "GSM861784", null, "source name:whole zebrafish embryos at 24 hpf|age:24 hpf|development stage:embryo|tissue:whole body|cell type:all cell types", "miRNA GFP minus", "The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2.", "whole zebrafish embryos at 24 hpf", "Tgkdrl:egfp embryos were dissociated at 24 hpf  followed by fluorescence activated cell sorting to isolate GFP positive and  negative cells.", "Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters  followed by cDNA synthesis and amplification with Illumina primers.", null, "age:24 hpf|developmental stage:embryo|tissue:whole body|cell type:all cell types", "GSM861784", "GSM861784: miRNA GFP minus; Danio rerio; RNA Seq", "GSM861784 1", "GSM861784: miRNA GFP minus", "1", null, "GEO Accession:GSM861784", "RNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", "<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>", "SRP010291", null, null, "miRNA_CNTL_WT.fastq.gz", "fastq", 295021332.0, 8195037.0, "GSM861784 r1", "0:36", "A:70414178;C:53495749;G:76994313;T:87833261;N:6283831", 36, null, null, null, 70414178, 53495749, 76994313, 87833261, 6283831, "SRX115580", "SRS285697", "SRA049243", "GEO", "Nathan Lawson Lab, PGFE, Umass Medical School", 1, 0.02832, null, 0.02716, null, 0.99957, null, 0.43137, null, 36, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2012-01-12", "Pharyngula", "Embryo", "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.", null, "pubmed:26694924", null, "fins", "GSM1630515", null, "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", null, "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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 28\u00baC 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", null, "1", "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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", null, "SRP056014", null, null, null, null, 113161.0, 2108.0, "GSM1630515 r1", "0:4 1:49.68", "A:30303;C:30710;G:27210;T:24785;N:153", 4, 49, null, null, 30303, 30710, 27210, 24785, 153, "SRX915251", "SRS870223", "SRA246117", "GEO", "University of Aveiro", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 50, null, "T", null, "under 1.2% mapping rate", "legacy", "early", "3prime", "size_fractionation", "unknown", "bulk", "other_seq", "454", null, "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.", null, "pubmed:26694924", null, "skin", "GSM1630514", null, "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", null, "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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 28\u00baC 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", null, "1", "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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", null, "SRP056014", null, null, null, null, 79232.0, 1527.0, "GSM1630514 r1", "0:4 1:47.89", "A:20622;C:23508;G:19017;T:15967;N:118", 4, 47, null, null, 20622, 23508, 19017, 15967, 118, "SRX915250", "SRS870224", "SRA246117", "GEO", "University of Aveiro", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 53, null, "T", null, "under 1.2% mapping rate", "legacy", "early", "3prime", "size_fractionation", "unknown", "bulk", "other_seq", "454", null, "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.", null, "pubmed:26694924", null, "adult", "GSM1630509", null, "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", null, "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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 28\u00baC 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", null, "1", "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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", null, "SRP056014", null, null, null, null, 361024.0, 6498.0, "GSM1630509 r1", "0:4 1:51.56", "A:104704;C:84406;G:83224;T:87843;N:847", 4, 51, null, null, 104704, 84406, 83224, 87843, 847, "SRX915245", "SRS870229", "SRA246117", "GEO", "University of Aveiro", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 51, null, "T", null, "under 1.2% mapping rate", "legacy", "early", "3prime", "size_fractionation", "unknown", "bulk", "other_seq", "454", null, "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.", null, "pubmed:26694924", null, "45dpf", "GSM1630508", null, "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", null, "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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 28\u00baC 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", null, "1", "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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", null, "SRP056014", null, null, null, null, 123960.0, 2248.0, "GSM1630508 r1", "0:4 1:51.14", "A:38130;C:31332;G:30088;T:24223;N:187", 4, 51, null, null, 38130, 31332, 30088, 24223, 187, "SRX915244", "SRS870230", "SRA246117", "GEO", "University of Aveiro", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 52, null, "T", null, "under 1.2% mapping rate", "legacy", "early", "3prime", "size_fractionation", "unknown", "bulk", "other_seq", "454", null, "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.", null, "pubmed:26694924", null, "5dpf", "GSM1630507", null, "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", null, "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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 28\u00baC 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", null, "1", "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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", null, "SRP056014", null, null, null, null, 168981.0, 3060.0, "GSM1630507 r1", "0:4 1:51.22", "A:51895;C:42870;G:40864;T:32741;N:611", 4, 51, null, null, 51895, 42870, 40864, 32741, 611, "SRX915243", "SRS870231", "SRA246117", "GEO", "University of Aveiro", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 50, null, "T", null, "under 1.2% mapping rate", "legacy", "early", "3prime", "size_fractionation", "unknown", "bulk", "other_seq", "454", null, "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.", null, "pubmed:26694924", null, "96hpf", "GSM1630506", null, "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", null, "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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 28\u00baC 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", null, "1", "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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", null, "SRP056014", null, null, null, null, 61235.0, 1109.0, "GSM1630506 r1", "0:4 1:51.22", "A:18594;C:15084;G:15091;T:12247;N:219", 4, 51, null, null, 18594, 15084, 15091, 12247, 219, "SRX915242", "SRS870232", "SRA246117", "GEO", "University of Aveiro", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 52, null, "T", null, "under 1.2% mapping rate", "legacy", "early", "3prime", "size_fractionation", "unknown", "bulk", "other_seq", "454", null, "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.", null, "pubmed:26694924", null, "72hpf", "GSM1630505", null, "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", null, "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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 28\u00baC 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", null, "1", "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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", null, "SRP056014", null, null, null, null, 778415.0, 14183.0, "GSM1630505 r1", "0:4 1:50.88", "A:231211;C:186354;G:190297;T:169348;N:1205", 4, 50, null, null, 231211, 186354, 190297, 169348, 1205, "SRX915241", "SRS870233", "SRA246117", "GEO", "University of Aveiro", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 48, null, "T", null, "under 1.2% mapping rate", "legacy", "early", "3prime", "size_fractionation", "unknown", "bulk", "other_seq", "454", null, "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.", null, "pubmed:26694924", null, "24hpf", "GSM1630504", null, "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", null, "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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 28\u00baC 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", null, "1", "100 \u03bcg of total RNA from each sample was isolated using TRIzol\u00ae 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\u00b0C  followed by phenol extraction. First strand cDNA synthesis was then performed using a specific three prime primer and Superscript\u2122 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\u00b0C 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", null, "SRP056014", null, null, null, null, 6831.0, 129.0, "GSM1630504 r1", "0:4 1:48.95", "A:1947;C:1747;G:1688;T:1424;N:25", 4, 48, null, null, 1947, 1747, 1688, 1424, 25, "SRX915240", "SRS870234", "SRA246117", "GEO", "University of Aveiro", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 46, null, "T", null, "under 1.2% mapping rate", "legacy", "early", "3prime", "size_fractionation", "unknown", "bulk", "other_seq", "454", null, "Portugal", "2015-03-09", "Pharyngula", "Embryo", "Trunk", "Surface Structure"], [41250, "SRR3987432", "SRX1989729", "SRS1593551", "SRP080353", "PRJNA335856", "High throughput sequencing analysis identify miRNAs in 7dpf F1 zebrafish under \u00df diketone antibiotics exposure to F0 zebrafish", "GSE85004", "Transcriptome Analysis", "Small RNA high throughput sequencing technology was used to characterize the miRNAs in F1 zebrafish post 90 day \u00df diketone\u00a0antibiotic DKA exposure to F0 zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7 dpf F1 zebrafish were constructed. In total  10 117 347  9 818 830 and 12 049 949 raw reads were acquired  respectively  under the different DKA exposure treatments 0  6.25 mg/L and 12.5mg/L from the three miRNAs libraries by Illumina sequencing. Low quality reads were removed  which included five prime' contaminants  those missing the three prime' primer or insert tag  sequences with a poly A tail  and those shorter than 17 nt and longer than 25 nt. As a result  8 141 146 representing 312 735 unique sequences; control  8 687 210 representing 251 508 unique sequences; 6.25 mg/L  and 10 569 566 representing 441 938 unique sequences; 12.5 mg/L valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar  and the unique sRNA reads were mainly distributed in the 20 24 nt range  among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads  respectively. The 22 nt sRNAs were the most abundant  with the length distribution of counts of sequ seqs and unique miRNAs displaying a normal distribution. Overall design: Sample 1: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 12.5 mg/L.", null, null, null, "S12 F1", "GSM2255739", null, "source name:F1 zebrafish  7 dpf  F0 12.5 mg/L DKA exposure|strain/background:AB|genotype/variation:WT|f0 treatment:12.5 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf", "S12 F1", "Briefly  the raw reads were subjected to the Illumina pipeline filter Solexa 0.3  and then the dataset was further processed with an in house program  ACGT101 miR LC Sciences  Houston  Texas  USA  to remove adapter dimers  junk  low complexity  common RNA families rRNA  tRNA  snRNA  snoRNA and repeats. Subsequently  unique sequences with length in 1826 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p  and 5p derived miRNAs. Length variation at both 3\u2019 and 5\u2019 ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p  or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 20.0 by BLAST search  and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes  and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software http://rna.tbi.univie.ac.at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem <=12; 2 number of base pairs in the stem region of the predicted hairpin >=16; 3 cutoff of free energy kCal/mol <=15; 4 length of hairpin up and down stems + terminal loop >=50; 5 length of hairpin loop <=20; 6 number of nucleotides in one bulge in mature region <=8; 7 number of biased errors in one bulge in mature region<=4; 8 number of biased bulges in mature region <=2; 9 number of errors in mature region <=7; 10 number of base pairs in the mature region of the predicted hairpin >=12; and 11 percent of mature in stem >=80. For normalized abundance measurements  a modified global normalization is used to correct copy numbers among different samples. Basic assumptions and procedures involved in this method are: 1. There is a subset of sequences of a significant number that do not change significantly across all samples. 2. In sequencing measurements  experimental condition variations may lead to copy number reading variations. However  in each sample run  the reading variations occur in the same proportion to all sequences. This assumption permits the use of a single correction factor for all sequences in a sample. Genome build: Zv9 ftp://ftp.ensembl.org/pub/release 66/fasta/danio rerio/dna/ Supplementary files format and content: Table8.2 S12 F1vsS6 F1vsCON F1.xlsx indicates the differential expression between two DKA exposure treatments 6.25 and 12.5 mg/L treatments and control. Supplementary files format and content: Table8.6 S12 F1vsS6 F1.xlsx indicates the differential expression between 6.25 mg/L and 12.5 mg/L DKA exposure treatments. Supplementary files format and content: Table8.7 S6 F1vsCON F1.xlsx indicates the differential expression between 6.25 mg/L DKA exposure treatment and control. Supplementary files format and content: Table8.8 S12 F1vsCON F1.xlsx indicates the differential expression between 12.5 mg/L DKA exposure treatment and control.", "F1 zebrafish  7 dpf  F0 12.5 mg/L DKA exposure", "Adult wild type zebrafish AB strain were purchased from a local supplier. Embryos at 6 hpf were exposed to control and two DKA treatments 6.25 and 12.5 mg/L composed of a mix of the six DKA species listed below with equal weight concentrations and equal volumes of each DKA species. post 90 days of DKA exposure  F1 zebrafish at 7 dpf for each group control and two DKA exposure treatments were collected. Certified DKA reference standards were sourced from Amresco Solon  OH  USA and used as received: ofluoxacin CAS No. 82419 36 1  purity of 99%  ciprofloxacin 85721 33 1  99%  enrofloxacin 93106 60 6  99%  doxycycline 24390 14 5  99%  chlortetracycline 64 72 2  95% and oxytetracycline 79 57 2  99%.", "Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer\u2019s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. Approximately 1 \u03bcg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina  San Diego  USA. Then  we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou  China following the vendor\u2019s recommended protocol.", null, "strain/background:AB|genotype/variation:WT|f0 treatment:12.5 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf", "GSM2255739", "GSM2255739: S12 F1; Danio rerio; ncRNA Seq", "GSM2255739", null, "1", "Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer\u2019s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. Approximately 1 \u03bcg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina  San Diego  USA. Then  we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou  China following the vendor\u2019s recommended protocol.", "GEO Accession:GSM2255739", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP080353", null, null, "S12_F1.fq", "fastq", 602497450.0, 12049949.0, "GSM2255739 r1", "0:50", "A:147750395;C:138369661;G:162147841;T:153975593;N:253960", 50, null, null, null, 147750395, 138369661, 162147841, 153975593, 253960, "SRX1989729", "SRS1593551", "SRA446490", "GEO", "Wenzhou Medical University Chashan Campus Chashan University Town, Wenzhou, Zhejiang Province", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-29", "Larval", "Larval", "Trunk", "Surface Structure"], [41251, "SRR3987431", "SRX1989728", "SRS1593550", "SRP080353", "PRJNA335856", "High throughput sequencing analysis identify miRNAs in 7dpf F1 zebrafish under \u00df diketone antibiotics exposure to F0 zebrafish", "GSE85004", "Transcriptome Analysis", "Small RNA high throughput sequencing technology was used to characterize the miRNAs in F1 zebrafish post 90 day \u00df diketone\u00a0antibiotic DKA exposure to F0 zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7 dpf F1 zebrafish were constructed. In total  10 117 347  9 818 830 and 12 049 949 raw reads were acquired  respectively  under the different DKA exposure treatments 0  6.25 mg/L and 12.5mg/L from the three miRNAs libraries by Illumina sequencing. Low quality reads were removed  which included five prime' contaminants  those missing the three prime' primer or insert tag  sequences with a poly A tail  and those shorter than 17 nt and longer than 25 nt. As a result  8 141 146 representing 312 735 unique sequences; control  8 687 210 representing 251 508 unique sequences; 6.25 mg/L  and 10 569 566 representing 441 938 unique sequences; 12.5 mg/L valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar  and the unique sRNA reads were mainly distributed in the 20 24 nt range  among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads  respectively. The 22 nt sRNAs were the most abundant  with the length distribution of counts of sequ seqs and unique miRNAs displaying a normal distribution. Overall design: Sample 1: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 12.5 mg/L.", null, null, null, "S6 F1", "GSM2255738", null, "source name:F1 zebrafish  7 dpf  F0 6.25 mg/L DKA exposure|strain/background:AB|genotype/variation:WT|f0 treatment:6.25 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf", "S6 F1", "Briefly  the raw reads were subjected to the Illumina pipeline filter Solexa 0.3  and then the dataset was further processed with an in house program  ACGT101 miR LC Sciences  Houston  Texas  USA  to remove adapter dimers  junk  low complexity  common RNA families rRNA  tRNA  snRNA  snoRNA and repeats. Subsequently  unique sequences with length in 1826 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p  and 5p derived miRNAs. Length variation at both 3\u2019 and 5\u2019 ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p  or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 20.0 by BLAST search  and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes  and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software http://rna.tbi.univie.ac.at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem <=12; 2 number of base pairs in the stem region of the predicted hairpin >=16; 3 cutoff of free energy kCal/mol <=15; 4 length of hairpin up and down stems + terminal loop >=50; 5 length of hairpin loop <=20; 6 number of nucleotides in one bulge in mature region <=8; 7 number of biased errors in one bulge in mature region<=4; 8 number of biased bulges in mature region <=2; 9 number of errors in mature region <=7; 10 number of base pairs in the mature region of the predicted hairpin >=12; and 11 percent of mature in stem >=80. For normalized abundance measurements  a modified global normalization is used to correct copy numbers among different samples. Basic assumptions and procedures involved in this method are: 1. There is a subset of sequences of a significant number that do not change significantly across all samples. 2. In sequencing measurements  experimental condition variations may lead to copy number reading variations. However  in each sample run  the reading variations occur in the same proportion to all sequences. This assumption permits the use of a single correction factor for all sequences in a sample. Genome build: Zv9 ftp://ftp.ensembl.org/pub/release 66/fasta/danio rerio/dna/ Supplementary files format and content: Table8.2 S12 F1vsS6 F1vsCON F1.xlsx indicates the differential expression between two DKA exposure treatments 6.25 and 12.5 mg/L treatments and control. Supplementary files format and content: Table8.6 S12 F1vsS6 F1.xlsx indicates the differential expression between 6.25 mg/L and 12.5 mg/L DKA exposure treatments. Supplementary files format and content: Table8.7 S6 F1vsCON F1.xlsx indicates the differential expression between 6.25 mg/L DKA exposure treatment and control. Supplementary files format and content: Table8.8 S12 F1vsCON F1.xlsx indicates the differential expression between 12.5 mg/L DKA exposure treatment and control.", "F1 zebrafish  7 dpf  F0 6.25 mg/L DKA exposure", "Adult wild type zebrafish AB strain were purchased from a local supplier. Embryos at 6 hpf were exposed to control and two DKA treatments 6.25 and 12.5 mg/L composed of a mix of the six DKA species listed below with equal weight concentrations and equal volumes of each DKA species. post 90 days of DKA exposure  F1 zebrafish at 7 dpf for each group control and two DKA exposure treatments were collected. Certified DKA reference standards were sourced from Amresco Solon  OH  USA and used as received: ofluoxacin CAS No. 82419 36 1  purity of 99%  ciprofloxacin 85721 33 1  99%  enrofloxacin 93106 60 6  99%  doxycycline 24390 14 5  99%  chlortetracycline 64 72 2  95% and oxytetracycline 79 57 2  99%.", "Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer\u2019s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. Approximately 1 \u03bcg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina  San Diego  USA. Then  we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou  China following the vendor\u2019s recommended protocol.", null, "strain/background:AB|genotype/variation:WT|f0 treatment:6.25 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf", "GSM2255738", "GSM2255738: S6 F1; Danio rerio; ncRNA Seq", "GSM2255738", null, "1", "Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer\u2019s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. Approximately 1 \u03bcg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina  San Diego  USA. Then  we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou  China following the vendor\u2019s recommended protocol.", "GEO Accession:GSM2255738", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP080353", null, null, "S6_F1.fq", "fastq", 490941500.0, 9818830.0, "GSM2255738 r1", "0:50", "A:119942635;C:111532763;G:133144810;T:126303825;N:17467", 50, null, null, null, 119942635, 111532763, 133144810, 126303825, 17467, "SRX1989728", "SRS1593550", "SRA446490", "GEO", "Wenzhou Medical University Chashan Campus Chashan University Town, Wenzhou, Zhejiang Province", 1, 1e-05, null, 0.0, null, 1.0, null, null, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-29", "Larval", "Larval", "Trunk", "Surface Structure"], [41252, "SRR3987430", "SRX1989727", "SRS1593549", "SRP080353", "PRJNA335856", "High throughput sequencing analysis identify miRNAs in 7dpf F1 zebrafish under \u00df diketone antibiotics exposure to F0 zebrafish", "GSE85004", "Transcriptome Analysis", "Small RNA high throughput sequencing technology was used to characterize the miRNAs in F1 zebrafish post 90 day \u00df diketone\u00a0antibiotic DKA exposure to F0 zebrafish at 6.25 and 12.5 mg/L. The small RNA libraries from 7 dpf F1 zebrafish were constructed. In total  10 117 347  9 818 830 and 12 049 949 raw reads were acquired  respectively  under the different DKA exposure treatments 0  6.25 mg/L and 12.5mg/L from the three miRNAs libraries by Illumina sequencing. Low quality reads were removed  which included five prime' contaminants  those missing the three prime' primer or insert tag  sequences with a poly A tail  and those shorter than 17 nt and longer than 25 nt. As a result  8 141 146 representing 312 735 unique sequences; control  8 687 210 representing 251 508 unique sequences; 6.25 mg/L  and 10 569 566 representing 441 938 unique sequences; 12.5 mg/L valid reads in the 17 to 25 nt size range were isolated for further analysis. The sRNAs from the three libraries were similar  and the unique sRNA reads were mainly distributed in the 20 24 nt range  among which 22 and 23 nt accounted for 41.8% and 20.0% of total unique sRNA reads  respectively. The 22 nt sRNAs were the most abundant  with the length distribution of counts of sequ seqs and unique miRNAs displaying a normal distribution. Overall design: Sample 1: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 0 mg/L; Sample 2: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 6.25 mg/L; Sample 3: Examination of small RNA in 7 dpf F1 zebrafish post 90 day DKA exposure to F0 zebrafish at 12.5 mg/L.", null, null, null, "CON F1", "GSM2255737", null, "source name:F1 zebrafish  7 dpf  F0 0 mg/L DKA exposure|strain/background:AB|genotype/variation:WT|f0 treatment:0 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf", "CON F1", "Briefly  the raw reads were subjected to the Illumina pipeline filter Solexa 0.3  and then the dataset was further processed with an in house program  ACGT101 miR LC Sciences  Houston  Texas  USA  to remove adapter dimers  junk  low complexity  common RNA families rRNA  tRNA  snRNA  snoRNA and repeats. Subsequently  unique sequences with length in 1826 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p  and 5p derived miRNAs. Length variation at both 3\u2019 and 5\u2019 ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA containing arm were considered to be novel 5p  or 3p derived miRNA candidates. The remaining sequences were mapped to other selected species precursors with the exclusion of specific species in miRBase 20.0 by BLAST search  and the mapped pre miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes  and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software http://rna.tbi.univie.ac.at/cgi bin/RNAfold.cgi. The criteria for secondary structure prediction were: 1 number of nucleotides in one bulge in stem <=12; 2 number of base pairs in the stem region of the predicted hairpin >=16; 3 cutoff of free energy kCal/mol <=15; 4 length of hairpin up and down stems + terminal loop >=50; 5 length of hairpin loop <=20; 6 number of nucleotides in one bulge in mature region <=8; 7 number of biased errors in one bulge in mature region<=4; 8 number of biased bulges in mature region <=2; 9 number of errors in mature region <=7; 10 number of base pairs in the mature region of the predicted hairpin >=12; and 11 percent of mature in stem >=80. For normalized abundance measurements  a modified global normalization is used to correct copy numbers among different samples. Basic assumptions and procedures involved in this method are: 1. There is a subset of sequences of a significant number that do not change significantly across all samples. 2. In sequencing measurements  experimental condition variations may lead to copy number reading variations. However  in each sample run  the reading variations occur in the same proportion to all sequences. This assumption permits the use of a single correction factor for all sequences in a sample. Genome build: Zv9 ftp://ftp.ensembl.org/pub/release 66/fasta/danio rerio/dna/ Supplementary files format and content: Table8.2 S12 F1vsS6 F1vsCON F1.xlsx indicates the differential expression between two DKA exposure treatments 6.25 and 12.5 mg/L treatments and control. Supplementary files format and content: Table8.6 S12 F1vsS6 F1.xlsx indicates the differential expression between 6.25 mg/L and 12.5 mg/L DKA exposure treatments. Supplementary files format and content: Table8.7 S6 F1vsCON F1.xlsx indicates the differential expression between 6.25 mg/L DKA exposure treatment and control. Supplementary files format and content: Table8.8 S12 F1vsCON F1.xlsx indicates the differential expression between 12.5 mg/L DKA exposure treatment and control.", "F1 zebrafish  7 dpf  F0 0 mg/L DKA exposure", "Adult wild type zebrafish AB strain were purchased from a local supplier. Embryos at 6 hpf were exposed to control and two DKA treatments 6.25 and 12.5 mg/L composed of a mix of the six DKA species listed below with equal weight concentrations and equal volumes of each DKA species. post 90 days of DKA exposure  F1 zebrafish at 7 dpf for each group control and two DKA exposure treatments were collected. Certified DKA reference standards were sourced from Amresco Solon  OH  USA and used as received: ofluoxacin CAS No. 82419 36 1  purity of 99%  ciprofloxacin 85721 33 1  99%  enrofloxacin 93106 60 6  99%  doxycycline 24390 14 5  99%  chlortetracycline 64 72 2  95% and oxytetracycline 79 57 2  99%.", "Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer\u2019s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. Approximately 1 \u03bcg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina  San Diego  USA. Then  we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou  China following the vendor\u2019s recommended protocol.", null, "strain/background:AB|genotype/variation:WT|f0 treatment:0 mg/L DKA exposure for 90 days|tissue:F1 whole body|f1 developmental stage:7 dpf", "GSM2255737", "GSM2255737: CON F1; Danio rerio; ncRNA Seq", "GSM2255737", null, "1", "Total RNA was extracted using Trizol reagent Invitrogen  CA  USA following the manufacturer\u2019s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit Agilent  CA  USA with RIN number >7.0. Approximately 1 \u03bcg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits Illumina  San Diego  USA. Then  we performed the single end sequencing 36 bp on an Illumina HiSeq 2500 at the LC BIO Hangzhou  China following the vendor\u2019s recommended protocol.", "GEO Accession:GSM2255737", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP080353", null, null, "CON_F1.fq", "fastq", 505867350.0, 10117347.0, "GSM2255737 r1", "0:50", "A:123471791;C:114424623;G:138931875;T:129020913;N:18148", 50, null, null, null, 123471791, 114424623, 138931875, 129020913, 18148, "SRX1989727", "SRS1593549", "SRA446490", "GEO", "Wenzhou Medical University Chashan Campus Chashan University Town, Wenzhou, Zhejiang Province", 1, 2e-05, null, 0.0, null, 0.99993, null, 0.66666, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2016-07-29", "Larval", "Larval", "Trunk", "Surface Structure"], [49015, "SRR7613129", "SRX4477829", "SRS3603028", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 100 ZF skin smallRNAseq", "GSM3309731", null, "source name:skin|strain:AB JxT\\xFC|tissue:skin|age:6 month|Sex:male", "NH FLI 100 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:skin|age:6 month|Sex:male", "GSM3309731", "GSM3309731: NH FLI 100 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309731", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309731", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 1018240050.0, 20364801.0, "GSM3309731 r1", "0:50", "A:207814229;C:262063346;G:311334117;T:236957867;N:70491", 50, null, null, null, 207814229, 262063346, 311334117, 236957867, 70491, "SRX4477829", "SRS3603028", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.1074, null, 0.00618, null, 0.9906, null, 0.54934, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49016, "SRR7613128", "SRX4477828", "SRS3603027", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 111 ZF skin smallRNAseq", "GSM3309730", null, "source name:skin|strain:AB JxT\\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male", "NH FLI 111 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male", "GSM3309730", "GSM3309730: NH FLI 111 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309730", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309730", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 356381250.0, 7127625.0, "GSM3309730 r1", "0:50", "A:70456264;C:88928211;G:109830748;T:87141036;N:24991", 50, null, null, null, 70456264, 88928211, 109830748, 87141036, 24991, "SRX4477828", "SRS3603027", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.12249, null, 0.00713, null, 0.99299, null, 0.51987, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49017, "SRR7613127", "SRX4477827", "SRS3603046", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 109 ZF skin smallRNAseq", "GSM3309729", null, "source name:skin|strain:AB JxT\\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male", "NH FLI 109 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male", "GSM3309729", "GSM3309729: NH FLI 109 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309729", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309729", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 591923400.0, 11838468.0, "GSM3309729 r1", "0:50", "A:118873766;C:162031990;G:180619895;T:130356928;N:40821", 50, null, null, null, 118873766, 162031990, 180619895, 130356928, 40821, "SRX4477827", "SRS3603046", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.09696, null, 0.00911, null, 0.99133, null, 0.52082, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49018, "SRR7613126", "SRX4477826", "SRS3603047", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 108 ZF skin smallRNAseq", "GSM3309728", null, "source name:skin|strain:AB JxT\\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male", "NH FLI 108 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male", "GSM3309728", "GSM3309728: NH FLI 108 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309728", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309728", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 736154900.0, 14723098.0, "GSM3309728 r1", "0:50", "A:138956520;C:196877364;G:231633259;T:168650452;N:37305", 50, null, null, null, 138956520, 196877364, 231633259, 168650452, 37305, "SRX4477826", "SRS3603047", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01397, null, 0.0029, null, 0.99312, null, 0.79541, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49019, "SRR7613125", "SRX4477825", "SRS3603026", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 107 ZF skin smallRNAseq", "GSM3309727", null, "source name:skin|strain:AB JxT\\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male", "NH FLI 107 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male", "GSM3309727", "GSM3309727: NH FLI 107 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309727", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309727", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 749544400.0, 14990888.0, "GSM3309727 r1", "0:50", "A:141473710;C:216076836;G:236230720;T:155730665;N:32469", 50, null, null, null, 141473710, 216076836, 236230720, 155730665, 32469, "SRX4477825", "SRS3603026", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.03825, null, 0.00867, null, 0.99439, null, 0.74015, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49020, "SRR7613124", "SRX4477824", "SRS3603024", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 106 ZF skin smallRNAseq", "GSM3309726", null, "source name:skin|strain:AB JxT\\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male", "NH FLI 106 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgwt1a:GFP|tissue:skin|age:3.5 years|Sex:male", "GSM3309726", "GSM3309726: NH FLI 106 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309726", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309726", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 611281450.0, 12225629.0, "GSM3309726 r1", "0:50", "A:111669012;C:149529261;G:189562873;T:160496848;N:23456", 50, null, null, null, 111669012, 149529261, 189562873, 160496848, 23456, "SRX4477824", "SRS3603024", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.02484, null, 0.00442, null, 0.9936, null, 0.64597, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49021, "SRR7613123", "SRX4477823", "SRS3603023", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 150 ZF skin smallRNAseq", "GSM3309725", null, "source name:skin|strain:AB JxT\\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male", "NH FLI 150 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male", "GSM3309725", "GSM3309725: NH FLI 150 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309725", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309725", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 2447513950.0, 48950279.0, "GSM3309725 r1", "0:50", "A:468043633;C:693473223;G:731577603;T:554251791;N:167700", 50, null, null, null, 468043633, 693473223, 731577603, 554251791, 167700, "SRX4477823", "SRS3603023", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.07052, null, 0.01139, null, 0.99263, null, 0.59059, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49022, "SRR7613122", "SRX4477822", "SRS3603025", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 149 ZF skin smallRNAseq", "GSM3309724", null, "source name:skin|strain:AB JxT\\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male", "NH FLI 149 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male", "GSM3309724", "GSM3309724: NH FLI 149 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309724", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309724", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 1871316900.0, 37426338.0, "GSM3309724 r1", "0:50", "A:380496272;C:509217150;G:560916561;T:420592548;N:94369", 50, null, null, null, 380496272, 509217150, 560916561, 420592548, 94369, "SRX4477822", "SRS3603025", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.03136, null, 0.00816, null, 0.99488, null, 0.79162, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49023, "SRR7613121", "SRX4477821", "SRS3603022", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 147 ZF skin smallRNAseq", "GSM3309723", null, "source name:skin|strain:AB JxT\\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male", "NH FLI 147 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male", "GSM3309723", "GSM3309723: NH FLI 147 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309723", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309723", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 445551200.0, 8911024.0, "GSM3309723 r1", "0:50", "A:89205774;C:110497307;G:135908107;T:109919980;N:20032", 50, null, null, null, 89205774, 110497307, 135908107, 109919980, 20032, "SRX4477821", "SRS3603022", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01905, null, 0.00266, null, 0.99504, null, 0.62127, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49024, "SRR7613120", "SRX4477820", "SRS3603021", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 146 ZF skin smallRNAseq", "GSM3309722", null, "source name:skin|strain:AB JxT\\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male", "NH FLI 146 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male", "GSM3309722", "GSM3309722: NH FLI 146 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309722", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309722", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 982200100.0, 19644002.0, "GSM3309722 r1", "0:50", "A:192209302;C:247406918;G:306793998;T:235751163;N:38719", 50, null, null, null, 192209302, 247406918, 306793998, 235751163, 38719, "SRX4477820", "SRS3603021", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.02155, null, 0.00424, null, 0.99368, null, 0.62937, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49025, "SRR7613119", "SRX4477819", "SRS3603020", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 145 ZF skin smallRNAseq", "GSM3309721", null, "source name:skin|strain:AB JxT\\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male", "NH FLI 145 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgpu.1:GFP|tissue:skin|age:3 years|Sex:male", "GSM3309721", "GSM3309721: NH FLI 145 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309721", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309721", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 1336985700.0, 26739714.0, "GSM3309721 r1", "0:50", "A:257049527;C:368876598;G:422514962;T:288505412;N:39201", 50, null, null, null, 257049527, 368876598, 422514962, 288505412, 39201, "SRX4477819", "SRS3603020", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.04358, null, 0.00841, null, 0.99312, null, 0.76026, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49026, "SRR7613118", "SRX4477818", "SRS3603019", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 137 ZF skin smallRNAseq", "GSM3309720", null, "source name:skin|strain:AB JxT\\xFC|tissue:skin|age:2 years|Sex:male", "NH FLI 137 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:skin|age:2 years|Sex:male", "GSM3309720", "GSM3309720: NH FLI 137 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309720", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309720", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 1039359300.0, 20787186.0, "GSM3309720 r1", "0:50", "A:200252400;C:286646217;G:322574775;T:229813195;N:72713", 50, null, null, null, 200252400, 286646217, 322574775, 229813195, 72713, "SRX4477818", "SRS3603019", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.10832, null, 0.00654, null, 0.99113, null, 0.52929, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49027, "SRR7613117", "SRX4477817", "SRS3603018", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 136 ZF skin smallRNAseq", "GSM3309719", null, "source name:skin|strain:AB JxT\\xFC|tissue:skin|age:2 years|Sex:male", "NH FLI 136 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:skin|age:2 years|Sex:male", "GSM3309719", "GSM3309719: NH FLI 136 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309719", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309719", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 858942900.0, 17178858.0, "GSM3309719 r1", "0:50", "A:168340182;C:217323317;G:266544838;T:206688895;N:45668", 50, null, null, null, 168340182, 217323317, 266544838, 206688895, 45668, "SRX4477817", "SRS3603018", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.00791, null, 0.00151, null, 0.99439, null, 0.71291, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49028, "SRR7613116", "SRX4477816", "SRS3603017", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 135 ZF skin smallRNAseq", "GSM3309718", null, "source name:skin|strain:AB JxT\\xFC|tissue:skin|age:2 years|Sex:male", "NH FLI 135 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:skin|age:2 years|Sex:male", "GSM3309718", "GSM3309718: NH FLI 135 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309718", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309718", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 1468015400.0, 29360308.0, "GSM3309718 r1", "0:50", "A:275374756;C:419939586;G:454098567;T:318538086;N:64405", 50, null, null, null, 275374756, 419939586, 454098567, 318538086, 64405, "SRX4477816", "SRS3603017", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01694, null, 0.00341, null, 0.99511, null, 0.72261, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49029, "SRR7613115", "SRX4477815", "SRS3603016", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 134 ZF skin smallRNAseq", "GSM3309717", null, "source name:skin|strain:AB JxT\\xFC|tissue:skin|age:2 years|Sex:male", "NH FLI 134 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:skin|age:2 years|Sex:male", "GSM3309717", "GSM3309717: NH FLI 134 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309717", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309717", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 678693700.0, 13573874.0, "GSM3309717 r1", "0:50", "A:137270784;C:164359833;G:207871154;T:169165189;N:26740", 50, null, null, null, 137270784, 164359833, 207871154, 169165189, 26740, "SRX4477815", "SRS3603016", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.02269, null, 0.00427, null, 0.99295, null, 0.61091, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49030, "SRR7613114", "SRX4477814", "SRS3603015", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 133 ZF skin smallRNAseq", "GSM3309716", null, "source name:skin|strain:AB JxT\\xFC|tissue:skin|age:2 years|Sex:male", "NH FLI 133 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:skin|age:2 years|Sex:male", "GSM3309716", "GSM3309716: NH FLI 133 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309716", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309716", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 847740400.0, 16954808.0, "GSM3309716 r1", "0:50", "A:168475291;C:220114466;G:260254419;T:198870005;N:26219", 50, null, null, null, 168475291, 220114466, 260254419, 198870005, 26219, "SRX4477814", "SRS3603015", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.02431, null, 0.00324, null, 0.99226, null, 0.63318, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49031, "SRR7613113", "SRX4477813", "SRS3603014", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 125 ZF skin smallRNAseq", "GSM3309715", null, "source name:skin|strain:AB JxT\\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male", "NH FLI 125 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male", "GSM3309715", "GSM3309715: NH FLI 125 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309715", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309715", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 1020735000.0, 20414700.0, "GSM3309715 r1", "0:50", "A:205383345;C:253177983;G:308564152;T:253535814;N:73706", 50, null, null, null, 205383345, 253177983, 308564152, 253535814, 73706, "SRX4477813", "SRS3603014", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.10278, null, 0.00523, null, 0.99155, null, 0.53907, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49032, "SRR7613112", "SRX4477812", "SRS3603012", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 122 ZF skin smallRNAseq", "GSM3309714", null, "source name:skin|strain:AB JxT\\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male", "NH FLI 122 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male", "GSM3309714", "GSM3309714: NH FLI 122 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309714", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309714", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 647896400.0, 12957928.0, "GSM3309714 r1", "0:50", "A:130330780;C:160929346;G:200383433;T:156218597;N:34244", 50, null, null, null, 130330780, 160929346, 200383433, 156218597, 34244, "SRX4477812", "SRS3603012", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.00732, null, 0.0014, null, 0.99401, null, 0.68357, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49033, "SRR7613111", "SRX4477811", "SRS3603013", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 121 ZF skin smallRNAseq", "GSM3309713", null, "source name:skin|strain:AB JxT\\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male", "NH FLI 121 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male", "GSM3309713", "GSM3309713: NH FLI 121 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309713", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309713", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 1387064850.0, 27741297.0, "GSM3309713 r1", "0:50", "A:262170854;C:395102028;G:446088168;T:283643764;N:60036", 50, null, null, null, 262170854, 395102028, 446088168, 283643764, 60036, "SRX4477811", "SRS3603013", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01646, null, 0.00363, null, 0.9922, null, 0.73895, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49034, "SRR7613110", "SRX4477810", "SRS3603011", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 120 ZF skin smallRNAseq", "GSM3309712", null, "source name:skin|strain:AB JxT\\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male", "NH FLI 120 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male", "GSM3309712", "GSM3309712: NH FLI 120 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309712", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309712", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 771712600.0, 15434252.0, "GSM3309712 r1", "0:50", "A:154765175;C:193689306;G:236383702;T:186844174;N:30243", 50, null, null, null, 154765175, 193689306, 236383702, 186844174, 30243, "SRX4477810", "SRS3603011", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.02376, null, 0.00465, null, 0.99166, null, 0.64918, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49035, "SRR7613109", "SRX4477809", "SRS3603010", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 119 ZF skin smallRNAseq", "GSM3309711", null, "source name:skin|strain:AB JxT\\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male", "NH FLI 119 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC Tgflk:mCherry|tissue:skin|age:1 year|Sex:male", "GSM3309711", "GSM3309711: NH FLI 119 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309711", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309711", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 582866200.0, 11657324.0, "GSM3309711 r1", "0:50", "A:113005827;C:152497718;G:181963234;T:135381588;N:17833", 50, null, null, null, 113005827, 152497718, 181963234, 135381588, 17833, "SRX4477809", "SRS3603010", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.02894, null, 0.00364, null, 0.99208, null, 0.58438, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49036, "SRR7613108", "SRX4477808", "SRS3603008", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 98 ZF skin smallRNAseq", "GSM3309710", null, "source name:skin|strain:AB JxT\\xFC|tissue:skin|age:6 month|Sex:male", "NH FLI 98 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:skin|age:6 month|Sex:male", "GSM3309710", "GSM3309710: NH FLI 98 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309710", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309710", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 663294800.0, 13265896.0, "GSM3309710 r1", "0:50", "A:137734100;C:161855118;G:201382193;T:162288125;N:35264", 50, null, null, null, 137734100, 161855118, 201382193, 162288125, 35264, "SRX4477808", "SRS3603008", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.00618, null, 0.00111, null, 0.99478, null, 0.65659, null, 50, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49037, "SRR7613107", "SRX4477807", "SRS3603009", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 96 ZF skin smallRNAseq", "GSM3309709", null, "source name:skin|strain:AB JxT\\xFC|tissue:skin|age:6 month|Sex:male", "NH FLI 96 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:skin|age:6 month|Sex:male", "GSM3309709", "GSM3309709: NH FLI 96 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309709", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309709", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 569130200.0, 11382604.0, "GSM3309709 r1", "0:50", "A:116615049;C:147340637;G:176081367;T:129067210;N:25937", 50, null, null, null, 116615049, 147340637, 176081367, 129067210, 25937, "SRX4477807", "SRS3603009", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.01763, null, 0.00207, null, 0.99389, null, 0.63527, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49038, "SRR7613106", "SRX4477806", "SRS3603007", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 94 ZF skin smallRNAseq", "GSM3309708", null, "source name:skin|strain:AB JxT\\xFC|tissue:skin|age:6 month|Sex:male", "NH FLI 94 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:skin|age:6 month|Sex:male", "GSM3309708", "GSM3309708: NH FLI 94 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309708", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309708", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 941640450.0, 18832809.0, "GSM3309708 r1", "0:50", "A:181731779;C:249059327;G:290464823;T:220348739;N:35782", 50, null, null, null, 181731779, 249059327, 290464823, 220348739, 35782, "SRX4477806", "SRS3603007", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.03203, null, 0.00641, null, 0.98993, null, 0.72488, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [49039, "SRR7613105", "SRX4477805", "SRS3603006", "SRP155559", "PRJNA483229", "Sequencing of Danio rerio skin for 5 age groups", "GSE117820", "Transcriptome Analysis", "Comparison of temporal small RNA gene expression profiles from Danio rerio skin. The smallRNA seq data comprise 5 age groups at 6  12  24  36 month and 42 month.    Jena Centre for Systems Biology of Ageing   JenAge www.jenage.de Overall design: 25 samples in 5 groups: 6 month 5 samples  12 month 5 samples  24 month 5 samples  36 month 5 samples  42 month 5 samples.", null, null, null, "NH FLI 85 ZF skin smallRNAseq", "GSM3309707", null, "source name:skin|strain:AB JxT\\xFC|tissue:skin|age:6 month|Sex:male", "NH FLI 85 ZF skin smallRNAseq", "Sequence information was extracted in FastQ format using CASAVA software 1.8.4 data processing step. Reads were trimmed und filtered using trimmomatic 0.36 [parameter: ILLUMINACLIP:smallRNAAdapter:2:6:6 LEADING:15 SLIDINGWINDOW:4:15 MINLEN:20]. Reads were mapped using BWA 0.7.12 r1039 [parameter:  n 0  o 0  e 0  l 8  k 0]. Reads per gene were counted using samtools 1.3.1 9 ge5dfb0a. Genome build: mirBase Release 21 D. rerio sequences only Supplementary files format and content: The Excel file includes raw counts sample counts.xls of all mirBase D. rerio sequences for each sample.", "skin", null, "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", null, "strain:AB JxT\\xFC|tissue:skin|age:6 month|Sex:male", "GSM3309707", "GSM3309707: NH FLI 85 ZF skin smallRNAseq; Danio rerio; ncRNA Seq", "GSM3309707", null, "1", "Extraction was done as described in Baumgart et al. 2012. PMID:22487494 Library preparation was done using Illumina's TruSeq smallRNA Library Preparation Kit following the manufacturer's instruction.", "GEO Accession:GSM3309707", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP155559", null, null, null, null, 974950550.0, 19499011.0, "GSM3309707 r1", "0:50", "A:188952378;C:263095911;G:305812761;T:217059876;N:29624", 50, null, null, null, 188952378, 263095911, 305812761, 217059876, 29624, "SRX4477805", "SRS3603006", "SRA745967", "GEO", "Leibniz Institute for Age Research - Fritz Lipmann Institute", 1, 0.03216, null, 0.00571, null, 0.99015, null, 0.67028, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "Germany", "2018-07-27", "Adult", "Adult", "Skin", "Surface Structure"], [61688, "SRR13302966", "SRX9731824", "SRS7924603", "SRP290217", "PRJNA673345", "Zebrafish as an animal model for the antiviral RNA interference pathway", "GSE160475", "Transcriptome Analysis", "We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV  vesicular stomatitis virus VSV  and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs  the hallmark of antiviral RNAi  with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile  the suppressor of RNAi VSR protein  NoV B2  may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.", null, null, null, "NoV\u25b3B2: Ago2 IP 3 dpi", "GSM4988099", null, "source name:zebrafish whole body|zebrafish background:AB|infection:NoV\u25b3B2|injection way:microinjection|tissue:zebrafish whole body", "NoV\u25b3B2: Ago2 IP 3 dpi", "Sequenced reads were trimmed for adaptor sequence  then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2", "zebrafish whole body", null, "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", null, "zebrafish background:AB|infection:NoV\u25b3B2|injection way:microinjection|tissue:zebrafish whole body", "GSM4988099", "GSM4988099: NoV\u25b3B2: Ago2 IP 3 dpi; Danio rerio; ncRNA Seq", "GSM4988099", null, "1", "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", "GEO Accession:GSM4988099", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP290217", null, null, "LY272.fq.gz", "fastq", 2608504950.0, 17390033.0, "GSM4988099 r1", "0:150 1:0", "A:741941121;C:669191911;G:747181676;T:450096994;N:93248", 150, 0, null, null, 741941121, 669191911, 747181676, 450096994, 93248, "SRX9731824", "SRS7924603", "SRA1151114", "GEO", "Fudan University", 1, 0.13133, null, 0.03425, null, 0.96802, null, 0.60095, null, 150, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-12-24", "Undetermined", "Larval", "Trunk", "Surface Structure"], [61689, "SRR12951276", "SRX9404383", "SRS7622158", "SRP290217", "PRJNA673345", "Zebrafish as an animal model for the antiviral RNA interference pathway", "GSE160475", "Transcriptome Analysis", "We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV  vesicular stomatitis virus VSV  and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs  the hallmark of antiviral RNAi  with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile  the suppressor of RNAi VSR protein  NoV B2  may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.", null, null, null, "SINV: zebrafish 3 dpi", "GSM4873784", null, "source name:zebrafish whole body|tissue:whole body|infection:SINV|injection way:microinjection|zebrafish background:AB", "SINV: zebrafish 3 dpi", "Sequenced reads were trimmed for adaptor sequence  then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2", "zebrafish whole body", null, "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", null, "tissue:whole body|infection:SINV|injection way:microinjection|zebrafish background:AB", "GSM4873784", "GSM4873784: SINV: zebrafish 3 dpi; Danio rerio; ncRNA Seq", "GSM4873784", null, "1", "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", "GEO Accession:GSM4873784", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP290217", null, null, "4_LY215.fq.gz", "fastq", 1328044600.0, 26560892.0, "GSM4873784 r1", "0:50 1:0", "A:383401484;C:303337306;G:339848340;T:301397824;N:59646", 50, 0, null, null, 383401484, 303337306, 339848340, 301397824, 59646, "SRX9404383", "SRS7622158", "SRA1151114", "GEO", "Fudan University", 1, 0.83242, null, 0.11559, null, 0.93634, null, 0.53516, null, 50, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-10-30", "Undetermined", "Larval", "Trunk", "Surface Structure"], [61690, "SRR12951275", "SRX9404382", "SRS7622159", "SRP290217", "PRJNA673345", "Zebrafish as an animal model for the antiviral RNA interference pathway", "GSE160475", "Transcriptome Analysis", "We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV  vesicular stomatitis virus VSV  and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs  the hallmark of antiviral RNAi  with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile  the suppressor of RNAi VSR protein  NoV B2  may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.", null, null, null, "VSV: zebrafish 24 hpi", "GSM4873783", null, "source name:zebrafish whole body|tissue:whole body|infection:VSV|injection way:microinjection|zebrafish background:AB", "VSV: zebrafish 24 hpi", "Sequenced reads were trimmed for adaptor sequence  then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2", "zebrafish whole body", null, "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", null, "tissue:whole body|infection:VSV|injection way:microinjection|zebrafish background:AB", "GSM4873783", "GSM4873783: VSV: zebrafish 24 hpi; Danio rerio; ncRNA Seq", "GSM4873783", null, "1", "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", "GEO Accession:GSM4873783", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP290217", null, null, "3_LY157.fq.gz", "fastq", 706147852.0, 29418915.0, "GSM4873783 r1", "0:24.00 1:0", "A:151681768;C:131117267;G:189016204;T:234316361;N:16252", 24, 0, null, null, 151681768, 131117267, 189016204, 234316361, 16252, "SRX9404382", "SRS7622159", "SRA1151114", "GEO", "Fudan University", 1, 0.92973, null, 0.12628, null, 0.90664, null, 0.45104, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-10-30", "Undetermined", "Larval", "Trunk", "Surface Structure"], [61691, "SRR12951274", "SRX9404381", "SRS7622157", "SRP290217", "PRJNA673345", "Zebrafish as an animal model for the antiviral RNA interference pathway", "GSE160475", "Transcriptome Analysis", "We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV  vesicular stomatitis virus VSV  and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs  the hallmark of antiviral RNAi  with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile  the suppressor of RNAi VSR protein  NoV B2  may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.", null, null, null, "NoV\u25b3B2: zebrafish 24 hpi", "GSM4873782", null, "source name:zebrafish whole body|tissue:whole body|infection:NoV{delta}B2|injection way:microinjection|zebrafish background:AB", "NoV\u25b3B2: zebrafish 24 hpi", "Sequenced reads were trimmed for adaptor sequence  then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2", "zebrafish whole body", null, "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", null, "tissue:whole body|infection:NoV{delta}B2|injection way:microinjection|zebrafish background:AB", "GSM4873782", "GSM4873782: NoV\u25b3B2: zebrafish 24 hpi; Danio rerio; ncRNA Seq", "GSM4873782", null, "1", "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", "GEO Accession:GSM4873782", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP290217", null, null, "2_LY156.fq.gz", "fastq", 748544818.0, 30779865.0, "GSM4873782 r1", "0:24.32 1:0", "A:166631198;C:138321792;G:208615021;T:234953337;N:23470", 24, 0, null, null, 166631198, 138321792, 208615021, 234953337, 23470, "SRX9404381", "SRS7622157", "SRA1151114", "GEO", "Fudan University", 1, 0.94115, null, 0.12368, null, 0.91076, null, 0.48684, null, 23, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-10-30", "Undetermined", "Larval", "Trunk", "Surface Structure"], [61692, "SRR12951273", "SRX9404380", "SRS7622156", "SRP290217", "PRJNA673345", "Zebrafish as an animal model for the antiviral RNA interference pathway", "GSE160475", "Transcriptome Analysis", "We have evaluated the possible use of zebrafish to study antiviral RNAi with sindbis virus SINV  vesicular stomatitis virus VSV  and nodamura virus NoV. We find that SINV and NoV viruses induce the production of virus derived small interfering RNAs vsiRNAs  the hallmark of antiviral RNAi  with a preference of 22 nucleotides in length post infection of larval zebrafish. Meanwhile  the suppressor of RNAi VSR protein  NoV B2  may affect the accumulation of the NoV virus in zebrafish. Overall design: 5 virus derived small RNA from zebrafish infected with different viruses was detected by small RNA seq.", null, null, null, "NoV: zebrafish 24 hpi", "GSM4873781", null, "source name:zebrafish whole body|tissue:whole body|infection:NoV|injection way:microinjection|zebrafish background:AB", "NoV: zebrafish 24 hpi", "Sequenced reads were trimmed for adaptor sequence  then mapped to virus genome using bowtie 1.1.2 with perfect match. Genome build: AF174533.1 AF174534.1;J02363.1;NC 001560.1 Supplementary files format and content: mapping results files generated by bowtie1.1.2", "zebrafish whole body", null, "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", null, "tissue:whole body|infection:NoV|injection way:microinjection|zebrafish background:AB", "GSM4873781", "GSM4873781: NoV: zebrafish 24 hpi; Danio rerio; ncRNA Seq", "GSM4873781", null, "1", "Total RNA was extracted from zebrafish using TRIzol reagent. Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.", "GEO Accession:GSM4873781", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP290217", null, null, "1_LY155.fq.gz", "fastq", 594676353.0, 25019145.0, "GSM4873781 r1", "0:23.77 1:0", "A:129139705;C:108465388;G:162500636;T:194556532;N:14092", 23, 0, null, null, 129139705, 108465388, 162500636, 194556532, 14092, "SRX9404380", "SRS7622156", "SRA1151114", "GEO", "Fudan University", 1, 0.93471, null, 0.10892, null, 0.90814, null, 0.48797, null, 22, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "China", "2020-10-30", "Undetermined", "Larval", "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", null, null, null, null, "BHEE H 3", null, "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", null, null, null, null, null, null, null, null, "miRNA Seq of zebrafish larvae", "AT20221124", "AT20221124", "miRNA Seq of zebrafish larvae", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "BGISEQ", "BGISEQ-500", null, "SRP402080", null, "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, null, null, null, 120057830, 104713991, 142506271, 166150296, 501, "SRX17856938", "SRS15377982", "SRA1518395", "Jiangsu University|School of Environment and Safety Engineering", "Jiangsu 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