{"database": "metadata", "table": "run_metadata", "rows": [[37221, "SRR1035984", "SRX381838", "SRS506055", "SRP033261", "PRJNA229539", "Whole transcriptomic sequencing of zebrafish rx3 mutants during optic vesicle morphogenesis", "GSE52652", "Transcriptome Analysis", "To identify genes regulated by Rx3 during optic vesicle morphogenesis  adult zebrafish carriers of a null rx3 mutation were mated. Before 13 hpf  the earliest time point at which optic vesicle evagination phenotypes could be reliably detected  offspring were phenotypically separated into pools comprising of mutants with an absence of optic vesicles or siblings exhibiting a wild type phenotype. Three replicates of pooled RNA samples from 13 hpf eyeless mutants rx3 /  or phenotypically wild type siblings rx3+/+ or rx3+/   and one replicate of 13 hpf wild type zebrafish larva were collected for whole transcriptome sequencing. Overall design: Whole transcriptome sequencing RNA seq was performed on zebrafish rx3 /  mutants  wild type siblings and wild type AB strains at 13 hpf", null, "pubmed:25266257", null, "Wild type AB strain rep1", "GSM1273590", null, "source name:Whole embryo|strain:AB|tissue:Whole embryo|age:13 hpf|genotype:Wild type AB strain", "Wild type AB strain rep1", "Due to low sequencing quality at 3\u2019 ends  RNA seq reads were trimmed at 40 bp. Reads were mapped to the zebrafish genome version 9 using TopHat. Novel transcripts were assembled by Cufflinks using mapped reads. Novel transcripts less than 300 bp were discarded. RNA seq reads were counted using HTSeq. Genome build: Zv9 Supplementary files format and content: counts.txt: Tab delimited text files include gene symbol  chromosome location and No. of mapped reads and RPKM for each sample.", "Whole embryo", null, "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "Zebrafish were handled according to standard protocols and animals studies were approved by the UCD Animal Research Ethics Committee AREC P 08 54. Heterozygous carriers of a recessive rx3 mutation chkw29 allele were mated. These fish originate from mutagenesis screens performed in AB zebrafish. Offspring were grown to the 13 hpf stage in embryo medium containing methylene blue at 28.5\u00b0C in 10 hour dark: 14 hour light cycle conditions. The eyeless mutant rx3 /  and eyed sibling wild type rx3+/+ and heterozygous rx3+/  carriers samples were distinguished based on their morphology using a dissecting light microscope at the 8 somite stage.", "strain:AB|tissue:Whole embryo|age:13 hpf|genotype:Wild type AB strain", "GSM1273590", "GSM1273590: Wild type AB strain rep1; Danio rerio; RNA Seq", "GSM1273590", null, "1", "Three biological replicates were collected for each sample and one replicate of wild type AB strain embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater Qiagen  Hilden  Germany and stored at 4\u00b0C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA  on column DNaseI digestion was performed and RNA was collected in RNase free water  as per manufacturer\u2019s instructions Qiagen  Hilden  Germany. A Nanodrop spectrophotometer Beckman  USA was used to determine the concentration of RNA and a Bioanalyser Agilent  Santa Clara  USA was used to confirm the RNA Integrity Number RIN of the samples as 8 or higher. Using 1 \u03bcg of total RNA  cDNA libraries were prepared using the mRNA seq 8 Sample Prep Kit as per manufacturer\u2019s instructions Illumina  RS 100 0801. Briefly  poly A containing mRNA molecules were purified using poly T oligo attached magnetic beads. Following purification  mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.", "GEO Accession:GSM1273590", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer II", null, "SRP033261", null, null, "WT.fastq", "fastq", 898405760.0, 22460144.0, "GSM1273590 r1", "0:40", "A:227899706;C:221325355;G:214303297;T:234727455;N:149947", 40, null, null, null, 227899706, 221325355, 214303297, 234727455, 149947, "SRX381838", "SRS506055", "SRA112080", "GEO", "Kennedy Lab, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin", 1, 0.941, null, 0.05403, null, 0.72023, null, 0.47159, null, 40, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "full_length", "poly_a", "unknown", "bulk", "bulk", "bulk", null, "Ireland", "2013-11-22", "Segmentation", "Embryo", "Whole Organism", "All anatomical structures"]], "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": ["rowid"], "primary_key_values": ["37221"], "units": {}, "query_ms": 12.47181800135877}