{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation = \"Pharyngula\" and experiment.library_strategy = \"ncRNA-Seq\"", "rows": [[36266, "SRR953577", "SRX336218", "SRS471213", "SRP028895", "PRJNA138095", "Transcriptome wide analysis of small RNA expression in early zebrafish development", "GSE27722", "Transcriptome Analysis", "During early vertebrate development  a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription.  The exact identity  expression levels  and function during early vertebrate development for most of these noncoding RNAs remains largely unknown.  miRNAs microRNAs and piRNAs piwi interacting RNAs are two classes of small non coding RNAs that play important roles in gene regulation during early embryonic development.  Here  we utilized Illumina next generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system.  For miRNAs  the expression patterns for 192 known miRNAs and 12 novel miRNAs within 123 different miRNA families were determined.  Significant sequence variation was observed at the five prime' and three prime' ends of miRNAs with a large number of extra nucleotides added in a non template directed manner.  We also identified a large and diverse set of piRNAs expressed during early development  far beyond that expected if piRNA expression is restricted to germ cells.  Our analyses represent the deepest investigation to date of small RNA expression during early vertebrate development and suggest important novel functions for small RNAs during embryogenesis. Overall design: Identify the expression of small RNAs in zebrafish embryos of four different developmental stages using high through put sequencing", null, "pubmed:22408181", null, "embryo 1dpf rep1", "GSM686385", null, "source name:the whole embryo|strain:AB*WT|developmental stage:1dpf|tissue:the whole embryos", "embryo 1dpf rep1", "fasta: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences. All the sequence with N inside was removed as well. The unique sequences were retained with the counts indicating thier abundance. The header of each sequence is composed of a unique sequence ID followed by a \" x\" and the reads counts. e.g. unique ID x counts. alignment: Initial reads were processed to remove linker sequences using a dynamic alignment algorithm  which allows one mismatch in the linker sequences.  Small RNAs with perfect matches to the zebrafish genome Zv8 from Ensembl http://www.ensembl.org were retrieved using megaBLAST http://www.ncbi.nlm.nih.gov/blast/megablast.shtml and Bowtie http://bowtie bio.sourceforge.net/tutorial.shtml. To identify piRNAs  consensus sequences from zebrafish repetitive elements were retrieved from Repbase http://www.girinst.org/repbase/index.html and Repeat Maskers using the UCSC genome browser http://genome.ucsc.edu.  Small RNAs perfectly mapping to these consensus sequences and their genomic flanking regions were sorted into piRNA libraries with up to 3 genomic mapping positions for each unique RNA sequence. fasta files description: small RNA 15 30 nt alignment file description: piRNA map to repetitive elements", "the whole embryo", null, "Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.", "Embryos were raised at 28\u00c2\u00b0C in egg water 0.03% Instant Ocean marine salt mix for the initial several hours of development", "strain:AB*WT|developmental stage:1dpf|tissue:the whole embryos", "GSM686385", "GSM686385: embryo 1dpf rep1; Danio rerio; ncRNA Seq", "GSM686385", null, "1", "Zebrafish embryos were collected at the 256 cell stage  sphere stage  shield stage  and 1dpf.  Total RNA was isolated from embryos using Trizol.  RNAs were fractionated on 15% denaturing polyacrylamide gels and small RNAs between 15 30 nucleotides were excised and purified.  cDNA libraries were generated using specific linkers and RT/PCR  as previously described.  Libraries were sequenced in the Genome Technology Core of Vanderbilt University using the Illumina sequencing platform.", "GEO Accession:GSM686385", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP028895", null, null, "GSM686385_1dpf_Raw.txt", "fastq", 293700240.0, 8158340.0, "GSM686385 r1", "0:36", "A:74642033;C:62153879;G:83836688;T:69542606;N:3525034", 36, null, null, null, 74642033, 62153879, 83836688, 69542606, 3525034, "SRX336218", "SRS471213", "SRA098146", "GEO", "Lee Lab, Molecular Biology, Mass General Hospital", 1, 0.00386, null, 0.00274, null, 0.99758, null, 0.53623, null, 36, null, "T", null, "under 1.2% mapping rate", "illumina", "early_illumina", "5prime", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "United States", "2011-03-07", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [55862, "SRR10863003", "SRX7533065", "SRS5972268", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 1dpf rep3", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "small RNA of Zebrafish: PGCs 1dpf", "imb ketting 2018 03 redl smRNA 03 20 1dpf PGCs rep3 S3.R1", "imb ketting 2018 03 redl smRNA 03 20 1dpf PGCs rep3 S3.R1", "Next Flex small RNA seq kit v3  from BIOO scientific  starting from 1ng of total RNA. Followed the protocol version  V16.06  diluting the adaptors  for ligation and using 25 PCR cycles for library amplification. The library was size selected using an 8% TBE gel  and the library fragments of 146 168bp corresponding to insert sizes of 18 40bp were recovered and purified.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_03_redl_smRNA_03_20_1dpf_PGCs_rep3_S3.R1.fastq.gz", "fastq", 3136475328.0, 37338992.0, "imb ketting 2018 03 redl smRNA 03 20 1dpf PGCs rep3 S3.R1.fastq.gz", "0:84 1:0", "A:743596563;C:770089055;G:796526363;T:826235723;N:27624", 84, 0, null, null, 743596563, 770089055, 796526363, 826235723, 27624, "SRX7533065", "SRS5972268", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 1, 0.00094, null, 2e-05, null, 0.999, null, 0.69871, null, 84, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [55872, "SRR10863015", "SRX7533055", "SRS5972267", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 1dpf rep2", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "small RNA of Zebrafish: PGCs 1dpf", "imb ketting 2018 03 redl smRNA 02 30 1dpf PGCs rep2 S2.R1", "imb ketting 2018 03 redl smRNA 02 30 1dpf PGCs rep2 S2.R1", "Next Flex small RNA seq kit v3  from BIOO scientific  starting from 1ng of total RNA. Followed the protocol version  V16.06  diluting the adaptors  for ligation and using 25 PCR cycles for library amplification. The library was size selected using an 8% TBE gel  and the library fragments of 146 168bp corresponding to insert sizes of 18 40bp were recovered and purified.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_03_redl_smRNA_02_30_1dpf_PGCs_rep2_S2.R1.fastq.gz", "fastq", 3186833832.0, 37938498.0, "imb ketting 2018 03 redl smRNA 02 30 1dpf PGCs rep2 S2.R1.fastq.gz", "0:84 1:0", "A:772047868;C:764764928;G:803857310;T:846133704;N:30022", 84, 0, null, null, 772047868, 764764928, 803857310, 846133704, 30022, "SRX7533055", "SRS5972267", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 1, 0.00072, null, 1e-05, null, 0.99922, null, 0.65573, null, 84, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [55887, "SRR10863028", "SRX7533040", "SRS5972265", "SRP241074", "PRJNA597223", "Danio rerio primordial germ cell expression pofiling", "PRJNA597223", "Whole Genome Sequencing", "Primordial germ cells PGCs are the precursors of germ cells  which migrate to the genital ridge during early development. Relatively little is known about PGCs post their migration. We studied this post migratory stage using microscopy and sequencing techniques. We found that many PGC specific genes  including genes known to induce PGC fate in the mouse  are only activated several days post migration. At this same timepoint  PGC nuclei become extremely gyrated  displaying general opening of chromatin and high levels of transcription. This is accompanied by changes in nuage morphology and expression of large loci  named PERLs  enriched for retro transposons and piRNAs. piRNA biogenesis signatures rise in this same period. Interestingly  no nuclear Piwi protein could be detected  indicating that the zebrafish piRNA pathway is fully cytoplasmic. Our data show that the post migratory stage of zebrafish PGCs holds many cues to both germ cell fate establishment and piRNA pathway activation.", null, null, "The vasa:eGFP line Kr\u00f8vel and Olsen  2002 was used to FACS sort PGCs at different timepoints. Embryos were collected and incubated with TrypLETM Express for 40 to 70 minutes  killed on ice and gently pippeted up and down with a glass pipet and/or a 200\u00b5l low retention pipet tip. post visual inspection  cell suspension was separated from trunks using a 100 \u00b5m siev. Following another 5 15 minutes of digestion  FCS was added to 10% of total volume. Cells were spun down at 500g for 5min at RT  washed with PBS  resuspended in PBS with 2% FCS  put on Ice and immediately subjected to FACS using a 85\u00b5m nozzle on a BD FACSAria III SORP Becton Dickinson. 1000 to 2500 cells were sorted directly into Trizol. RNA from sorted PGCs and whole embryos was extracted with Trizol and stored in MQ at  80\u00b0C until library preparation was done.", null, "wt PGCs 1dpf rep1", null, "strain:vasa:eGFP|isolate:not applicable|breed:TUE|cultivar:not applicable|ecotype:not applicable|age:1dpf|dev stage:Pharyngula period|sex:not applicable|tissue:germline|biological replicate:replicate 1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "small RNA of Zebrafish: PGCs 1dpf", "imb ketting 2018 03 redl smRNA 01 24 1dpf PGCs rep1 S1.R1", "imb ketting 2018 03 redl smRNA 01 24 1dpf PGCs rep1 S1.R1", "Next Flex small RNA seq kit v3  from BIOO scientific  starting from 1ng of total RNA. Followed the protocol version  V16.06  diluting the adaptors  for ligation and using 25 PCR cycles for library amplification. The library was size selected using an 8% TBE gel  and the library fragments of 146 168bp corresponding to insert sizes of 18 40bp were recovered and purified.", null, null, "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "NextSeq 550", null, "SRP241074", null, null, "imb_ketting_2018_03_redl_smRNA_01_24_1dpf_PGCs_rep1_S1.R1.fastq.gz", "fastq", 2999534160.0, 35708740.0, "imb ketting 2018 03 redl smRNA 01 24 1dpf PGCs rep1 S1.R1.fastq.gz", "0:84 1:0", "A:763136061;C:754741465;G:717861943;T:763766703;N:27988", 84, 0, null, null, 763136061, 754741465, 717861943, 763766703, 27988, "SRX7533040", "SRS5972265", "SRA1023320", "Rene Ketting group|Ketting Lab", "Rene Ketting group", 1, 0.00031, null, 0.0, null, 0.99945, null, 0.59259, null, 84, null, "T", null, "under 1.2% mapping rate", "illumina", "nextseq", "unknown", "size_fractionation", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2020-01-10", "Pharyngula", "Embryo", "Whole Organism", "All anatomical structures"], [58542, "SRR13652355", "SRX10049118", "SRS8212347", "SRP253438", "PRJNA613601", "five prime half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [small RNA Seq  ssDRIP seq]", "GSE147253", "Other", "five primetRFls are small tRNA fragments derived from five prime half of mature tRNAs. However  it is unknown whether five primetRFls could feed back to regulate tRNA biogenesis. Here we show that five primetRFlGly/GCC and five primetRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis  dynamics of five primetRFlGly/GCC and five primetRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. Morpholino mediated knockdown of five primetRFlGly/GCC or five primetRFlGlu/CTC down regulates tRNAGly/GCC or tRNAGlu/CTC levels respectively  and causes embryonic lethality that is efficiently rescued by co injection of properly refolded corresponding tRNA. In zebrafish embryos  tRNA:DNA and five primetRFl:DNA hybrids commonly exist on the template strand of tRNA genes. Mechanistically  unstable five primetRFl:DNA hybrid may prevent the formation of transcriptionally inhibitory stable tRNA:DNA hybrids on the same tRNA loci so as to facilitate tRNA genes transcription. The uncovered mechanism may be implicated in other physiological and pathological processes. Overall design: For small RNA sequencing   total RNA were extracted respectively from wildtype zebrafish embryos T\u00fcbingen Strain of 6 chosen stages  and then subjected to small RNA library preparation individually. To investigate the distribution and stability of R loop on genome  we performed ssDRIP seq with S9.6 antibody  which specifically recognize RNA:DNA hybrid.  Two replicates from wildtype embryos of 256c  sphere and shield stage were collected to perform ssDRIPseq. RNaseH pre treated genome DNA was used as negative control  which was also performed the standard ssDRIP seq procedure. Genomic DNA extracted from these samples were fragmentated by restriction enzymes  and then immunoprecipitated by S9.6 antibody.The ssDNA strands in RNA:DNA hybrids were purified and subjected to library preparation.", "parent bioproject:PRJNA753013", "pubmed:34797706", null, "24hpf ncRNA seq", "GSM5069285", null, "tissue:embryo|strain:Tubingen|developmental stage:24 hpf stage|treatement:no", "24hpf ncRNA seq", "For data processing  reads were quality checked by FastQCVersion 0.11.8  and adaptors were cut off by Cutadapt Version 1.16  and only reads that lay between 18 40 nt were kept. The reads of each sample were first aligned to different database by using Bowtie2  Version 2.3.4.1  count table was generated by featureCounts. Genome build: GRCz11 genome and cDNA   tRNA database GtRNAdb  GRCz11", "embryo", null, "For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube  and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific  15596018. The lysate was centrifuged at 12 000 rpm for 10 min  and the supernatant was collected and mixed with 200 \u03bcl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4\u2103  the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min  followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at  80\u2103 until all samples were collected. Two pretreatment steps were included: First  purified total RNAs were treated with T4 Polynucleotide Kinase NEB  M0201S with ATP for 30 min at 37\u2103  then purified by phenol: chloroform extraction. The aim of this step is removing the 2 3\u2019 cyclic phosphate group from the 3\u2019end of 5\u2019tRFls  and add phosphate group to the 5\u2019end of 3\u2019tRFs. In the second step  total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing:  Small RNA libraries  using 1 \u03bcg RNA each  were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research  then bands of 135 160 bp  about the length of 15 40 nt RNA ligated with both adaptors  were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc  pH 4.5  followed by precipitation by adding 2.5 volumes of ethanol.", null, "strain:Tubingen|developmental stage:24 hpf stage|treatement:no", "GSM5069285", "GSM5069285: 24hpf ncRNA seq; Danio rerio; ncRNA Seq", "GSM5069285", null, "1", "For small RNA sequencing: About 50 100 zebrafish eggs or embryos at a desired stage were dechorionated by Pronase digestion and collected to extract total RNA. Embryos were then transferred to 1.5 ml eppendorf tube  and lysed in 1 ml Trizol Reagent Thermo Fisher Scientific  15596018. The lysate was centrifuged at 12 000 rpm for 10 min  and the supernatant was collected and mixed with 200 \u03bcl chloroform in a fresh tube. post centrifugation at 12 000 rpm for 10 min at 4\u2103  the supernatant was transferred to a fresh tube with addition of equal volume of isopropanol and incubated at room temperature for 15 min  followed by thorough mix and centrifugation at 12 000 rpm for 10 20 min. The RNA pellet was washed by 75% ethanol once and was stored as pellet in 75% ethanol at  80\u2103 until all samples were collected. Two pretreatment steps were included: First  purified total RNAs were treated with T4 Polynucleotide Kinase NEB  M0201S with ATP for 30 min at 37\u2103  then purified by phenol: chloroform extraction. The aim of this step is removing the 2 three prime cyclic phosphate group from the three primeend of five primetRFls  and add phosphate group to the five primeend of three primetRFs. In the second step  total RNAs were treated with ALKB protein mix as mentioned above. Purified total RNAs were then subjected to small RNA library preparation. For small RNA sequencing:  Small RNA libraries  using 1 \u03bcg RNA each  were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina NEB according to the manual. The amplified DNA from each sample was first concentrated by DNA concentrator spin column Zymo Research  then bands of 135 160 bp  about the length of 15 40 nt RNA ligated with both adaptors  were manually selected on native PAGE gel. DNAs were eluted from the gel piece with 0.3 M NaOAc  pH 4.5  followed by precipitation by adding 2.5 volumes of ethanol.", "GEO Accession:GSM5069285", "ncRNA-Seq", "TRANSCRIPTOMIC", "size fractionation", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP253438", null, null, "24hpf-RNA_seq.fq.gz", "fastq", 4887202650.0, 32581351.0, "GSM5069285 r1", "0:150 1:0", "A:821306307;C:893949781;G:2431277343;T:739975843;N:693376", 150, 0, null, null, 821306307, 893949781, 2431277343, 739975843, 693376, "SRX10049118", "SRS8212347", "SRA1056877", "GEO", "Anming Meng Lab, School of Life Science, Tsinghua University", 1, 0.60067, null, 0.12422, null, 0.81132, null, 0.45351, null, 150, null, "B", null, "usable mapping rate", "illumina", "novaseq_era", "5prime", "size_fractionation", "nebnext", "bulk", "unknown", "unknown", null, "China", "2021-02-08", "Pharyngula", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "truncated": false, "filtered_table_rows_count": 5, "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": "ncRNA-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=ncRNA-Seq", "results": [{"value": "ncRNA-Seq", "label": "ncRNA-Seq", "count": 5, "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=ncRNA-Seq", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=ncRNA-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=ncRNA-Seq", "results": [{"value": "size fractionation", "label": "size fractionation", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=ncRNA-Seq&experiment.library_selection=size+fractionation", "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=ncRNA-Seq", "results": [{"value": "SINGLE", "label": "SINGLE", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=ncRNA-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=ncRNA-Seq", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=ncRNA-Seq&experiment.platform=ILLUMINA", "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=ncRNA-Seq", "results": [{"value": "Embryo", "label": "Embryo", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=ncRNA-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=ncRNA-Seq", "results": [{"value": "Pharyngula", "label": "Pharyngula", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?experiment.library_strategy=ncRNA-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=ncRNA-Seq", "results": [{"value": "All anatomical structures", "label": "All anatomical structures", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=ncRNA-Seq&tissue_curation_coarse=All+anatomical+structures", "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=ncRNA-Seq", "results": [{"value": "Whole Organism", "label": "Whole Organism", "count": 4, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=ncRNA-Seq&tissue_curation=Whole+Organism", "selected": false}, {"value": "Embryo Imprecise", "label": "Embryo Imprecise", "count": 1, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=ncRNA-Seq&tissue_curation=Embryo+Imprecise", "selected": false}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=ncRNA-Seq", "results": [{"value": "unknown", "label": "unknown", "count": 5, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation=Pharyngula&experiment.library_strategy=ncRNA-Seq&technology=unknown", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": null, "next_url": null, "private": false, "allow_execute_sql": true, "query_ms": 66.67459900199901}