{"database": "metadata", "table": "run_metadata", "rows": [[41512, "SRR5004962", "SRX2336796", "SRS1790194", "SRP092907", "PRJNA352850", "Transcriptomics analysis of gene expressions  m6A enrichment levels and ythdf2 binding targets in control and mettl3 or ythdf2 morphants zebrafish embryos", "GSE89655", "Other", "RNA was isolated from control and mettl3 or ythdf2 morphants zebrafish cells using the TRIzol Invitrogen reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN RNA integrity number of higher than 9. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq2500 or HiSeq 3000 Illumina in paired read mode  creating reads with a length of 101 or 151 bp. Sequencing chemistry v2 Illumina was used. Overall design: Examination of gene expressive levels  m6A enrichment levels  m6A single uncleotide sites and ythdf2 binding targets in normal and mettl3 or ythdf2 morphants zebrafish cells", null, "pubmed:28869969", null, "zebrafish embryos ythdf2 RIP rep1", "GSM2386191", null, "source name:zebrafish embryos|genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "zebrafish embryos ythdf2 RIP rep1", "Reads were aligned to the zv9 genome assembly using TopHat v2.0.9 For each sample  reads counts of all genes were computed using HTSeq v0.5.3p9 Genome build: zv9 Supplementary files format and content: reads count HTSeq.xls: Reads count for each gene of all samples Supplementary files format and content: ythdf2 binding target.xls: ythdf2 binding targets identified by macs2 software", "zebrafish embryos", null, "For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", null, "genotype/variation:normal|cell type:embryos cells|age:28hpf|tissue:trunk", "GSM2386191", "GSM2386191: zebrafish embryos ythdf2 RIP rep1; Danio rerio; RIP Seq", "GSM2386191", null, "1", "For RIP seq  RNA was isolate from ythdf2 Flag mRNA injected zebrafish embryos and the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 \u00b5g of total RNA was then used for library preparation using a TruSeq\u2122 RNA Sample Prep Kit v2 Illumina  San Diego  CA  USA according to the manufacturer\u2019s protocol.The libraries were sequenced using HiSeq3000 Illumina in paired read mode  creating reads with a length of 101 bp.", "GEO Accession:GSM2386191", "RIP-Seq", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP092907", null, null, "ythdf2_RIP_rep1_1.fastq.gz ythdf2_RIP_rep1_2.fastq.gz", "fastq fastq", 6144583662.0, 30418731.0, "GSM2386191 r1", "0:101 1:101", "A:1227614258;C:1869131844;G:1825793436;T:1220118819;N:1925305", 101, 101, null, null, 1227614258, 1869131844, 1825793436, 1220118819, 1925305, "SRX2336796", "SRS1790194", "SRA491654", "GEO", "Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)", 2, 0.96857, 0.96917, 0.23397, 0.22377, 0.89832, 0.90147, 0.78619, 0.8258, 101, 101, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "other", "trueseq", "bulk", "bulk", "bulk", null, "China", "2016-11-08", "Pharyngula", "Embryo", "Trunk", "Surface Structure"]], "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": ["41512"], "units": {}, "query_ms": 8.348290000867564}