{"database": "metadata", "table": "run_metadata", "rows": [[38053, "SRR1519895", "SRX657108", "SRS662288", "SRP044634", "PRJNA255636", "mRNA sequencing of embryonic tails of sih mutants at 28 hpf", "GSE59563", "Transcriptome Analysis", "We analysed the mRNA expression of embryos lacking blood flow at the onset of heart function. Overall design: Examination of 3 WT and 3 sih mutants at 28 hpf", null, null, null, "sih1", "GSM1439469", null, "tissue:tail derived cells|genotype/variation:sih|embryonic stage:28 hpf", "sih1", "Base calling : Image analysis and base calling were performed using the Illumina Pipeline version 1.6 Alignment : Reads were mapped to Zv9 assembly of zebrafish genome using Tophat v1.4 1 Quantification : Gene expression was quantified using HTSeq v0.5.3p5 and annotations from Ensembl release 69 Normalization : Data normalization was performed with edgeR v3.0.8 Bioconductor package Genome build: Zv9 Supplementary files format and content: The processed data file is a tabulated text with the following columns : Ensembl gene id  Gene name and one column for each sample containing the normalized read counts", "tail derived cells", "sih embryos lack heart contraction", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C  30 sec at 60\u00b0C  30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "Embryos were grown in normal conditions", "genotype/variation:sih|embryonic stage:28 hpf", "GSM1439469", "GSM1439469: sih1; Danio rerio; RNA Seq", "GSM1439469", null, "1", "RNA was extracted using TRIzol Invitrogen according to the manufacturer's instructions The library of template molecules suitable for high throughput DNA sequencing was created following the Illumina \u201cmRNA sequencing sample preparation guide\u201d part #1004898 Rev.D with some modifications. Briefly  mRNA was purified from 2 \u00b5g total RNA using oligo dT magnetic beads and fragmented using divalent cations at 94\u00b0C for 5 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers  then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The next steps of RNA Seq Library preparation were performed in a fully automated system using SPRIworks Fragment Library System I kit ref A84801  Beckman Coulter  Inc with the SPRI TE instrument Beckman Coulter  Inc. Briefly  in this system  double stranded cDNA fragments were blunted  phosphorylated and ligated to indexed adapter dimers  and fragments in the range of 200 400 bp were size selected. The automated steps were followed by PCR amplification 30 sec at 98\u00b0C; [10 sec at 98\u00b0C  30 sec at 60\u00b0C  30 sec at 72\u00b0C] x 13 cycles; 5 min at 72\u00b0C  then surplus PCR primers were removed by purification using AMPure XP beads Agencourt Biosciences Corporation. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer Agilent.", "GEO Accession:GSM1439469", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina Genome Analyzer IIx", null, "SRP044634", null, null, "JGZ-02.fastq.gz", "fastq", 1451212470.0, 26874305.0, "GSM1439469 r1", "0:54", "A:368354355;C:360129390;G:353350795;T:369317437;N:60493", 54, null, null, null, 368354355, 360129390, 353350795, 369317437, 60493, "SRX657108", "SRS662288", "SRA175990", "GEO", "IGBMC", 1, 0.94911, null, 0.04509, null, 0.74604, null, 0.46107, null, 54, null, "B", null, "usable mapping rate", "illumina", "early_illumina", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "France", "2014-07-18", "Pharyngula", "Embryo", "Tail", "Multi-system"]], "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": ["38053"], "units": {}, "query_ms": 12.252482993062586}