{"database": "metadata", "table": "run_metadata", "rows": [[53640, "SRR10004189", "SRX6742925", "SRS5293748", "SRP218844", "PRJNA560923", "Rbm24 functions as a critical translational regulator to pretect crystallin proteins accumulation for lens transparency. RNA seq data of 33 hpf rbm24a /  and wildtype embryo  head explant", "GSE136003", "Transcriptome Analysis", "This experiment is aimed to compare the transcriptomes of rbm24a mutant and wildtype at 33 hpf. As Rbm24a is an RNA binding protein  this comparation is suitable to obtain information on differential gene expression and alternative splicing. We found that the expression of most of the crystallin genes and many other lens specific genes are down regulated in rbm24a mutant  without xxx in splicing patterns. Overall design: It contains two groups: wildtype and rbm24a / . Wildtype was used as control", null, "pubmed:32170011", null, "R 1", "GSM4039262", null, "source name:head explant|dev stage:33 hpf|tissue:head region cut before otic vesicle|strain:AB|genotype/variation: 8 bp deletion by TALEN in the 1st exon", "R 1", "Base calling: Bcl2fastq v2.17.1.14 Data filtering step: Cutadapt\uff08version 1.9.1\uff09 Allignment: Hisat2v2.0.1  default parameter Differential gene expression: DESeq2\uff08V1.6.3\uff09 Gene expression: Htseq software V 0.6.1 Genome build: GRCz11 Supplementary files format and content: excel file  gene expression level in FPKM Supplementary files format and content: excel file  differentially expressed genes", "head explant", "the head region of 33 hpf embryos were cut and collected for RNA extraction", "Trizol and isopropanol precipitation The mRNA libraries were constructed by TruSeq RNA Library Preparation Kit  and 100 bp paired end sequencing was performed on Illumina HiSeq 2000. The data obtained from three independent samples were aligned and analysed as described Shao et al.  2017.", null, "dev stage:33 hpf|tissue:head region cut before otic vesicle|strain:AB|genotype/variation: 8 bp deletion by TALEN in the 1st exon", "GSM4039262", "GSM4039262: R 1; Danio rerio; RNA Seq", "GSM4039262", null, "1", "Trizol and isopropanol precipitation The mRNA libraries were constructed by TruSeq RNA Library Preparation Kit  and 100 bp paired end sequencing was performed on Illumina HiSeq 2000. The data obtained from three independent samples were aligned and analysed as described Shao et al.  2017.", "GEO Accession:GSM4039262", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP218844", null, null, "R1_combined_R1.fastq.gz R1_combined_R2.fastq.gz", "fastq fastq", 7918195500.0, 26393985.0, "GSM4039262 r1", "0:150 1:150", "A:2130539253;C:1816469246;G:1847209333;T:2123238120;N:739548", 150, 150, null, null, 2130539253, 1816469246, 1847209333, 2123238120, 739548, "SRX6742925", "SRS5293748", "SRA945259", "GEO", "School of Lifesciences, Shandong University", 2, 0.92358, 0.92932, 0.06139, 0.0616, 0.7218, 0.73192, 0.4833, 0.48317, 150, 150, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "China", "2019-08-19", "Pharyngula", "Embryo", "Head", "Nervous 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": ["53640"], "units": {}, "query_ms": 8.545493001292925}