{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Pharyngula\" and experiment.library_strategy = \"miRNA-Seq\"", "rows": [[38252, "SRR1593717", "SRX718003", "SRS713863", "SRP048545", "PRJNA262696", "Adenylation of maternally inherited microRNAs by Wispy", "GSE61931", "Other", "Early development depends heavily on accurate control of maternally inherited mRNAs  and yet it remains unknown how maternal microRNAs miRNAs are regulated during maternal to zygotic transition MZT. We here find that maternal miRNAs are highly adenylated at their three prime ends in mature oocytes and early embryos. Pervasive adenylation is observed in oocytes of fly  sea urchin and mouse  indicating that maternal miRNA adenylation may be widely conserved in animals. We identify Wispy as the enzyme responsible for miRNA adenylation in flies. Wispy is known to be expressed specifically in oocytes and early embryos and function as a noncanonical polyA polymerase. Knockout of wispy abrogates miRNA adenylation and induces miRNA accumulation in fly eggs whereas overexpression of Wispy increases adenylation and reduces miRNA levels in S2 cells. Adenylation occurs on both the 5p and 3p miRNAs  indicating that Wispy acts on miRNAs post Dicer processing. We further find that Wispy interacts with Ago1 through protein protein interaction  which may allow the effective and selective adenylation of miRNAs. Thus  adenylation may contribute to the clearance of maternally deposited miRNAs during MZT. Our work provides the first mechanistic insights into the regulation of maternal miRNAs and illustrates the importance of RNA tailing in development. Overall design: MiRNA expression and modification profile during early embryo development of fruit fly and zebra fish using high throughput sequencing", null, "pubmed:25454948", null, "Zeb fish Emb t 24h", "GSM1517418", null, "tissue:embryo|genotype/variation:WT|developmental stage:embryo 24h", "Zeb fish Emb t 24h", "The base calling was done by Illumina Pipeline CASAVA v1.8.2. The 3\u2032 adaptor sequences starting with \u201cTGGAATTC\u201d were removed  and the sequence reads with short length <16 nt or artifacts e.g. long homopolymer or low quality Phred quality <30 in >15% of nucleotides were filtered out using the FASTX Toolkit http://hannonlab.cshl.edu/fastx toolkit/. Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC  respectively. The BWA short read aligner Li and Durbin  2009 version 0.7.5a r405 was used for the alignment  with options of \u201818nt long seed length\u2019 and \u2018no allowed mismatches in the seed region. Each aligned read was classified using intersectBed in Bedtools Quinlan and Hall  2010 with annotations retrieved from RefSeq  GtRNAdb  FlyBase  RepeatMasker  Rfam  and miRBase. We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3\u2019 additions to the perfectly matching sequences. Sample wise normalization of miRNA read counts was done by TMM normalization Robinson and Oshlack  2010 using edgR package http://www.bioconductor.org/packages/release/bioc/html/edgeR.html. Genome build: dm3 GCF 000001215.2; danRer7 GCA 000002035.2 Supplementary files format and content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre processed reads of each class of RNA; dme miRNA TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA.  Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample.", "embryo", null, "Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer\u2019s guide. For each library  10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3\u2019 adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3\u2019 adaptor ligated RNA  the 5\u2019 adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.", null, "genotype/variation:WT|developmental stage:embryo 24h", "GSM1517418", "GSM1517418: Zeb fish Emb t 24h; Danio rerio; miRNA Seq", "GSM1517418", null, "1", "Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit Illumina according to manufacturer\u2019s guide. For each library  10 ug of total RNA was separated on 15% urea PAGE. RNA of 15 29 nt was gel purified and then ligated to the 3\u2019 adaptor with T4 RNA ligase2 truncated NEB. post gel purification of 3\u2019 adaptor ligated RNA  the 5\u2019 adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse transcribed by SuperScript II Life Technologies and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500. Total RNA was extracted using TRIzol reagent for each experimental condition.", "GEO Accession:GSM1517418", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP048545", null, null, "Zeb_fish_Emb_t_24h_1.fastq.gz", "fastq", 2747798604.0, 53878404.0, "GSM1517418 r1", "0:51", "A:675086979;C:579211488;G:812576920;T:680856005;N:67212", 51, null, null, null, 675086979, 579211488, 812576920, 680856005, 67212, "SRX718003", "SRS713863", "SRA188351", "GEO", "Narry Kim Lab, School of Biological Sciences, Seoul National University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 51, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "3prime", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "South Korea", "2014-09-30", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38323, "SRR1732705", "SRX822001", "SRS801696", "SRP051503", "PRJNA271079", "Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]", "GSE64465", "Transcriptome Analysis", "To investigate the complex regulatory networks disrupted in Holt Oram Syndrome  we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points  24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish  wild type AB strain line was used.", "parent bioproject:PRJNA271069", "pubmed:27471727", null, "Emb MO Ct 24hpf rep2", "GSM1571858", null, "source name:Embryos  MO Ct  24hpf  replicate2|tissue:embryo|strain:AB|treatment:Mo Ct injection|developmental stage:24hpf", "Emb MO Ct 24hpf rep2", "Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample", "Embryos  MO Ct  24hpf  replicate2", "1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino", "For each library 1 \u03bcg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc.  San Diego  USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 \u00b5l elution buffer Illumina for at least 2 hours at room temperature  to enrich for molecules containing inserts in the range of 18\u201333 nt.", "Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast  Varese  Italy.", "tissue:embryo|strain:AB|treatment:Mo Ct injection|developmental stage:24hpf", "GSM1571858", "GSM1571858: Emb MO Ct 24hpf rep2; Danio rerio; miRNA Seq", "GSM1571858", null, "1", "For each library 1 \u03bcg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc.  San Diego  USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 \u00b5l elution buffer Illumina for at least 2 hours at room temperature  to enrich for molecules containing inserts in the range of 18\u201333 nt.", "GEO Accession:GSM1571858", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP051503", null, null, "H.T.fq.gz", "fastq", 281909951.0, 10806197.0, "GSM1571858 r1", "0:26.09 1:0", "A:66055828;C:65184020;G:81768559;T:68892445;N:9099", 26, 0, null, null, 66055828, 65184020, 81768559, 68892445, 9099, "SRX822001", "SRS801696", "SRA221043", "GEO", "IIT, CNR", 1, 0.56084, null, 0.23499, null, 0.86819, null, 0.64638, null, 22, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Italy", "2014-12-23", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38324, "SRR1732704", "SRX822000", "SRS801695", "SRP051503", "PRJNA271079", "Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]", "GSE64465", "Transcriptome Analysis", "To investigate the complex regulatory networks disrupted in Holt Oram Syndrome  we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points  24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish  wild type AB strain line was used.", "parent bioproject:PRJNA271069", "pubmed:27471727", null, "Emb MO Ct 24hpf rep1", "GSM1571857", null, "source name:Embryos  MO Ct  24hpf  replicate1|tissue:embryo|strain:AB|treatment:Mo Ct injection|developmental stage:24hpf", "Emb MO Ct 24hpf rep1", "Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample", "Embryos  MO Ct  24hpf  replicate1", "1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino", "For each library 1 \u03bcg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc.  San Diego  USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 \u00b5l elution buffer Illumina for at least 2 hours at room temperature  to enrich for molecules containing inserts in the range of 18\u201333 nt.", "Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast  Varese  Italy.", "tissue:embryo|strain:AB|treatment:Mo Ct injection|developmental stage:24hpf", "GSM1571857", "GSM1571857: Emb MO Ct 24hpf rep1; Danio rerio; miRNA Seq", "GSM1571857", null, "1", "For each library 1 \u03bcg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc.  San Diego  USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 \u00b5l elution buffer Illumina for at least 2 hours at room temperature  to enrich for molecules containing inserts in the range of 18\u201333 nt.", "GEO Accession:GSM1571857", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP051503", null, null, "G.T.fq.gz", "fastq", 541546124.0, 19319535.0, "GSM1571857 r1", "0:28.03 1:0", "A:126881333;C:133281439;G:163930613;T:117435553;N:17186", 28, 0, null, null, 126881333, 133281439, 163930613, 117435553, 17186, "SRX822000", "SRS801695", "SRA221043", "GEO", "IIT, CNR", 1, 0.53436, null, 0.20796, null, 0.9009, null, 0.55394, null, 34, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Italy", "2014-12-23", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38325, "SRR1732703", "SRX821999", "SRS801694", "SRP051503", "PRJNA271079", "Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]", "GSE64465", "Transcriptome Analysis", "To investigate the complex regulatory networks disrupted in Holt Oram Syndrome  we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points  24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish  wild type AB strain line was used.", "parent bioproject:PRJNA271069", "pubmed:27471727", null, "Emb MO Tbx5a 24hpf rep2", "GSM1571856", null, "source name:Embryos  MO Tbx5a  24hpf  replicate2|tissue:embryo|strain:AB|treatment:Mo MOTbx5a injection|developmental stage:24hpf", "Emb MO Tbx5a 24hpf rep2", "Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample", "Embryos  MO Tbx5a  24hpf  replicate2", "1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino", "For each library 1 \u03bcg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc.  San Diego  USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 \u00b5l elution buffer Illumina for at least 2 hours at room temperature  to enrich for molecules containing inserts in the range of 18\u201333 nt.", "Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast  Varese  Italy.", "tissue:embryo|strain:AB|treatment:Mo MOTbx5a injection|developmental stage:24hpf", "GSM1571856", "GSM1571856: Emb MO Tbx5a 24hpf rep2; Danio rerio; miRNA Seq", "GSM1571856", null, "1", "For each library 1 \u03bcg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc.  San Diego  USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 \u00b5l elution buffer Illumina for at least 2 hours at room temperature  to enrich for molecules containing inserts in the range of 18\u201333 nt.", "GEO Accession:GSM1571856", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP051503", null, null, "F.T.fq.gz", "fastq", 362513460.0, 13684345.0, "GSM1571856 r1", "0:26.49 1:0", "A:82709386;C:83987865;G:107681867;T:88122760;N:11582", 26, 0, null, null, 82709386, 83987865, 107681867, 88122760, 11582, "SRX821999", "SRS801694", "SRA221043", "GEO", "IIT, CNR", 1, 0.58925, null, 0.2498, null, 0.86821, null, 0.65549, null, 30, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Italy", "2014-12-23", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [38326, "SRR1732702", "SRX821998", "SRS801693", "SRP051503", "PRJNA271079", "Discovering miRNA regulatory networks in Holt Oram Syndrome using a Zebrafish model [miRNA seq]", "GSE64465", "Transcriptome Analysis", "To investigate the complex regulatory networks disrupted in Holt Oram Syndrome  we characterized genome widely the miRNA and mRNA expression profiles in WT and Tbx5 depleted zebrafish embryos at two development time points  24 hpf and 48 hpf. Overall design: The zebrafish gene Tbx5a was silenced with antisense morpholino oligonucleotide MO Tbx5a against the TSS of the gene. A MO CT was used in CT samples. 1 5ng morpholinos were injected into the yolk of 1 cell stage embryos and total RNA extracted from xxx embryos collected at xxx and 48hpf.The Zebrafish  wild type AB strain line was used.", "parent bioproject:PRJNA271069", "pubmed:27471727", null, "Emb MO Tbx5a 24hpf rep1", "GSM1571855", null, "source name:Embryos  MO Tbx5a  24hpf  replicate1|tissue:embryo|strain:AB|treatment:Mo MOTbx5a injection|developmental stage:24hpf", "Emb MO Tbx5a 24hpf rep1", "Basecalls performed using CASAVA v1.8 Sequenced reads were trimmed for adaptor sequence. Reads were algned to miRBase v20 using miRExpress v2.1.3 Normalized abundance measurements from DESeq Genome build: miRBase v20 Supplementary files format and content: tab delimited text file includes normalized read count per sample", "Embryos  MO Tbx5a  24hpf  replicate1", "1 cell stage zebrafish embryos were microinjected with 1 5 ng of morpholino against dre Tbx5a MO Tbx5a or with 1 5 ng of control morpholino", "For each library 1 \u03bcg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc.  San Diego  USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 \u00b5l elution buffer Illumina for at least 2 hours at room temperature  to enrich for molecules containing inserts in the range of 18\u201333 nt.", "Zebrafish was raised and maintained under standard laboratory conditions Westerfileld M zebrafish book in Zebrafish Housing Systems Tecniplast  Varese  Italy.", "tissue:embryo|strain:AB|treatment:Mo MOTbx5a injection|developmental stage:24hpf", "GSM1571855", "GSM1571855: Emb MO Tbx5a 24hpf rep1; Danio rerio; miRNA Seq", "GSM1571855", null, "1", "For each library 1 \u03bcg of total RNA was submitted to the small RNA v1.5 sample preparation protocol llumina Inc.  San Diego  USA cDNA was amplified with 13 PCR cycle. cDNAs with size between 90 to 100 nt were purified independently for each sample by 10% Novex TBE polyacrylamide gel electrophoresis Invitrogen and eluted into 300 \u00b5l elution buffer Illumina for at least 2 hours at room temperature  to enrich for molecules containing inserts in the range of 18\u201333 nt.", "GEO Accession:GSM1571855", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP051503", null, null, "E.T.fq.gz", "fastq", 399134579.0, 13766109.0, "GSM1571855 r1", "0:28.99 1:0", "A:88725326;C:102855219;G:121123717;T:86418155;N:12162", 28, 0, null, null, 88725326, 102855219, 121123717, 86418155, 12162, "SRX821998", "SRS801693", "SRA221043", "GEO", "IIT, CNR", 1, 0.66472, null, 0.25948, null, 0.89623, null, 0.54913, null, 34, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Italy", "2014-12-23", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [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"], [40977, "SRR3498289", "SRX1756835", "SRS1433366", "SRP074848", "PRJNA321321", "microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues", "GSE81340", "Transcriptome Analysis", "Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "NoEndo 24hpf E1", "GSM2150814", null, "source name:Endothelial cell|developmental stage:24hpf|tissue:Endothelial|stain:GFP", "NoEndo 24hpf E1", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "Zebrafish embryos were raised according standard protocols at 28\u02daC and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.", "developmental stage:24hpf|tissue:Endothelial|stain:GFP", "GSM2150814", "GSM2150814: NoEndo 24hpf E1; Danio rerio; miRNA Seq", "GSM2150814", null, "1", "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2150814", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP074848", null, null, "NoEndo_24hpf_E1.fastq.gz", "fastq", 1422085704.0, 18711654.0, "GSM2150814 r1", "0:76", "A:347700492;C:356065333;G:376424133;T:341806001;N:89745", 76, null, null, null, 347700492, 356065333, 376424133, 341806001, 89745, "SRX1756835", "SRS1433366", "SRA424808", "GEO", "Internal Medicine, Yale University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-05-11", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [40983, "SRR3498283", "SRX1756829", "SRS1433360", "SRP074848", "PRJNA321321", "microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues", "GSE81340", "Transcriptome Analysis", "Proper functioning of tissues requires cells to behave in uniform  well organized ways. Conversely  many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here  we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably  lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate", "parent bioproject:PRJNA321317", "pubmed:28350988;pubmed:33273096", null, "Endo 24hpf E1", "GSM2150808", null, "source name:Endothelial cell|developmental stage:24hpf|tissue:Endothelial|stain:GFP", "Endo 24hpf E1", "Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence  and masked for low complexity or low quality sequence  then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software  Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ...", "Endothelial cell", null, "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "Zebrafish embryos were raised according standard protocols at 28\u02daC and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473.", "developmental stage:24hpf|tissue:Endothelial|stain:GFP", "GSM2150808", "GSM2150808: Endo 24hpf E1; Danio rerio; miRNA Seq", "GSM2150808", null, "1", "Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols", "GEO Accession:GSM2150808", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer", null, "SRP074848", null, null, "Endo_24hpf_E1.fastq.gz", "fastq", 1527500440.0, 20098690.0, "GSM2150808 r1", "0:76", "A:356712587;C:354608109;G:432977038;T:383106520;N:96186", 76, null, null, null, 356712587, 354608109, 432977038, 383106520, 96186, "SRX1756829", "SRS1433360", "SRA424808", "GEO", "Internal Medicine, Yale University", 1, 0.0, null, 0.0, null, 1.0, null, null, null, 76, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "unknown", "size_fractionation", "trueseq", "bulk", "unknown", "unknown", null, "United States", "2016-05-11", "Pharyngula", "Embryo", "Endothelium", "Cardiovascular System"], [41406, "SRR4423130", "SRX2245314", "SRS1745863", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 10 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:prim 16 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: prim 16 stage31 hpf", "348 10", "348 10", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S10small.fastq", "fastq", 427409571.0, 5026564.0, "S10small.fastq", "0:85.03", "A:98026046;C:116630773;G:114413502;T:98339250;N:0", 85, null, null, null, 98026046, 116630773, 114413502, 98339250, 0, "SRX2245314", "SRS1745863", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.81583, null, 0.17938, null, 0.9094, null, 0.63072, null, 126, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [41407, "SRR4423129", "SRX2245313", "SRS1745862", "SRP091534", "PRJNA347637", "Danio rerio and Xenopus laevis Raw sequence reads", "PRJNA347637", "Other", "To study the transcriptome during development", null, null, null, null, "Time course 9 Dr", null, "strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:prim 5 stage|sex:not determined|tissue:single embryo|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "miRNA Seq of Zebrafish: prim 5 stage24 hpf", "348 9", "348 9", "Libraries were generated according to the manufacturers\u2019 protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress\u2122 RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 \u00b5l ethanol instead of 120 \u00b5l during purification of cDNA and 134 \u00b5l ethanol instead of 110 \u00b5l in protocol.", null, null, "miRNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ION_TORRENT", "Ion Torrent Proton", null, "SRP091534", null, null, "S09small.fastq", "fastq", 516614705.0, 6246071.0, "S09small.fastq", "0:82.71", "A:117786535;C:140799134;G:139362428;T:118666608;N:0", 82, null, null, null, 117786535, 140799134, 139362428, 118666608, 0, "SRX2245313", "SRS1745862", "SRA485147", "Universiteit van Amsterdam|SILS", "Universiteit van Amsterdam", 1, 0.81132, null, 0.18952, null, 0.88925, null, 0.69719, null, 17, null, "B", null, "usable mapping rate", "ion_torrent", "ion_torrent", "unknown", "small_rna", "unknown", "bulk", "unknown", "unknown", null, "Netherlands", "2016-10-19", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"], [60887, "SRR12628234", "SRX9110497", "SRS7353480", "SRP282187", "PRJNA663091", "Characterization of small RNAs in early zebrafish PGCs", "GSE157865", "Transcriptome Analysis", "Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected  miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition  miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf  shield stage  11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs", null, "pubmed:33506864", null, "h24 2: PGCs 24hpf repeat2", "GSM4777194", null, "source name:PGCs|cell type:primordial germ cells|strain:AB|tissue:gonad", "h24 2: PGCs 24hpf repeat2", "Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample \u2026", "PGCs", null, "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", null, "cell type:primordial germ cells|strain:AB|tissue:gonad", "GSM4777194", "GSM4777194: h24 2: PGCs 24hpf repeat2; Danio rerio; miRNA Seq", "GSM4777194", null, "1", "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", "GEO Accession:GSM4777194", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP282187", null, null, "h24_2.fastq", "fastq", 4024398750.0, 26829325.0, "GSM4777194 r1", "0:150 1:0", "A:1030703487;C:1025857271;G:1004392553;T:963376583;N:68856", 150, 0, null, null, 1030703487, 1025857271, 1004392553, 963376583, 68856, "SRX9110497", "SRS7353480", "SRA1124474", "GEO", "Shanghai Institute of Biochemistry and Cell Biology,CAS", 1, 0.00025, null, 0.0, null, 0.99997, null, 1.0, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-12", "Pharyngula", "Embryo", "Gonad", "Reproductive System"], [60888, "SRR12628233", "SRX9110496", "SRS7353479", "SRP282187", "PRJNA663091", "Characterization of small RNAs in early zebrafish PGCs", "GSE157865", "Transcriptome Analysis", "Microscale small RNA high throughput sequencing was used to study small RNA distribution in early zebrafish PGCs primordial germ cells. We find that early zebrafish PGCs have large quantities of piRNAs and small quantities of miRNAs. Among the miRNAs detected  miR 430 accounted for the majority which has been proved to play diverse roles in zebrafish development. In addition  miR 92a 3p and miR 26a 5p have high expression and previous studies show that these two miRNAs can influence cell proliferation in cancer cells. More experiments should be performed in the future to explore whether miR 92a 3p and miR 26a 5p can influence the number of zebrafish PGCs. Overall design: Small RNA profiles at 6 hpf  shield stage  11 hpf 3 somite stage and 24 hpf prim 5 stage of zebrafish PGCs", null, "pubmed:33506864", null, "h24 1: PGCs 24hpf repeat1", "GSM4777193", null, "source name:PGCs|cell type:primordial germ cells|strain:AB|tissue:gonad", "h24 1: PGCs 24hpf repeat1", "Raw reads were pre processed by FASTX Toolkit version 0.0.14 1 Reads were mapped to danRer11 using bowtie version 1.0.0 5 miRNAs were quantified based on miRBase version 22.0 piRNAs were quantified using proTRAC version 2.2.0 Genome build: danRer11 Supplementary files format and content: tab delimited text file includes read number and RPM of miRNA expression for each sample \u2026", "PGCs", null, "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", null, "cell type:primordial germ cells|strain:AB|tissue:gonad", "GSM4777193", "GSM4777193: h24 1: PGCs 24hpf repeat1; Danio rerio; miRNA Seq", "GSM4777193", null, "1", "PGCs were picked out by green fluoresence small RNA seq library was constructed by microscale small RNA high throughput sequencing method.", "GEO Accession:GSM4777193", "miRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "HiSeq X Ten", null, "SRP282187", null, null, "h24_1.fastq", "fastq", 2223111450.0, 14820743.0, "GSM4777193 r1", "0:150 1:0", "A:510125618;C:561938103;G:577742482;T:573267493;N:37754", 150, 0, null, null, 510125618, 561938103, 577742482, 573267493, 37754, "SRX9110496", "SRS7353479", "SRA1124474", "GEO", "Shanghai Institute of Biochemistry and Cell Biology,CAS", 1, 0.0004, null, 0.0, null, 0.99993, null, 1.0, null, 150, null, "T", null, "under 1.2% mapping rate", "illumina", "hiseq_era", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "China", "2020-09-12", "Pharyngula", "Embryo", "Gonad", "Reproductive System"]], "truncated": false, "filtered_table_rows_count": 12, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation\" = :p0 and \"experiment.library_strategy\" = :p1 order by rowid limit 101", "params": {"p0": "Pharyngula", "p1": "miRNA-Seq"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq", "results": [{"value": "miRNA-Seq", "label": "miRNA-Seq", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula", "selected": true}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq", "results": [{"value": "size fractionation", "label": "size fractionation", "count": 10, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&experiment.library_selection=size+fractionation", "selected": false}, {"value": "cDNA", "label": "cDNA", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&experiment.library_selection=cDNA", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&experiment.platform=ILLUMINA", "selected": false}, {"value": "ION_TORRENT", "label": "ION_TORRENT", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&experiment.platform=ION_TORRENT", "selected": false}, {"value": "LS454", "label": "LS454", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&experiment.platform=LS454", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq", "results": [{"value": "Embryo", "label": "Embryo", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&devstage_curation_coarse=Embryo", "selected": false}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq", "results": [{"value": "Pharyngula", "label": "Pharyngula", "count": 12, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=miRNA-Seq", "selected": true}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 7, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&tissue_curation_coarse=All+anatomical+structures", "selected": false}, {"value": "Cardiovascular System", "label": "Cardiovascular System", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&tissue_curation_coarse=Cardiovascular+System", "selected": false}, {"value": "Reproductive System", "label": "Reproductive System", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&tissue_curation_coarse=Reproductive+System", "selected": false}, {"value": "Surface Structure", "label": "Surface Structure", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&tissue_curation_coarse=Surface+Structure", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq", "results": [{"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 7, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&tissue_curation=Embryo+Imprecise", "selected": false}, {"value": "Endothelium", "label": "Endothelium", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&tissue_curation=Endothelium", "selected": false}, {"value": "Gonad", "label": "Gonad", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&tissue_curation=Gonad", "selected": false}, {"value": "Trunk", "label": "Trunk", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&tissue_curation=Trunk", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq", "results": [{"value": "unknown", "label": "unknown", "count": 11, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&technology=unknown", "selected": false}, {"value": "454", "label": "454", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=miRNA-Seq&technology=454", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 101.05622600167408}