{"database": "metadata", "table": "run_metadata", "rows": [[38129, "SRR1555591", "SRX684699", "SRS687817", "SRP045679", "PRJNA258656", "Danio rerio high resolution developmental transcriptomic time course", "GSE60619", "Transcriptome Analysis", "Classical embryological studies revealed that during mid embryogenesis vertebrates show similar morphologies. This \u201cphylotypic stage\u201d has recently received support from transcriptome analyses  which have also detected similar stages in nematodes and arthropods. A conserved stage in these three phyla has led us to ask if all animals pass through a universal definitive stage as a consequence of ancestral constraints on animal development. Previous work has suggested that HOX genes may comprise such a \u2018zootypic\u2019 stage  however this hypothetical stage has hitherto resisted systematic analysis. We have examined the embryonic development of ten different animals each of a fundamentally different phylum  including a segmented worm  a flatworm  a roundworm  a water bear  a fruitfly  a sea urchin  a zebrafish  a sea anemone  a sponge  and a comb jelly. For each species  we collected the embryonic transcriptomes at 100 different developmental stages and analyzed their gene expression profiles. We found dynamic gene expression across all of the species that is structured in a stage like manner. Strikingly  we found that animal embryology contains two dominant modules of zygotic expression in terms of their protein domain composition: one involving proliferation  and a second involving differentiation. The switch between these two modules involves induction of the zootype; which in addition to homeobox containing genes  also involves Wnt and Notch signaling as well as forkhead domain transcription factors. Our results provide a systematic characterization of animal universality and identify the points of embryological constraints and flexibility. Overall design: 106 single embryo samples", "parent bioproject:PRJNA287810", "pubmed:26886793", null, "Metazome ZF timecourse sample 0099", "GSM1483834", null, "tissue:single embryo", "Metazome ZF timecourse sample 0099", "Libraries were sequenced on the Illumina HiSeq2000 according to standard  paired end sequencing  protocols. Primary analysis done in RTA 1.17.20 1.13.48 Conversion from BCL to FASTQ and deumltiplexing using CASAVA 1.8 configureBclToFastq.pl  fastq cluster count 1234567890   mismatches 0   use bases mask Y15n I6n Y35n Filter and read trimming barcode minimum quality of 10. trimming of read2 to 35 bases   not required. CEL Seq Hashimshony  et a. 2012l demultiplexing of second mate  using first mate barcode  allowing no mismatches in barcode. bowtie2  version 2.1.0  against Zv9 genome Read counting with htseq count version 0.5.4p3. Using on Ensemble Zv9 annotations Genome build: Zv9 Supplementary files format and content: tabular Expression matrix", "single embryo", null, "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "zebrafish fertilization was performed in the lab of Karina Yaniv Weizmann Institute  Israel. Four female and 1 male Danio rerio fish were mixed in a breeder tank and encouraged to spawn by tilting the tank and using artificial trees. post females started to release their eggs males quickly released sperm and fertilized eggs were collected into Zebrafish embryo medium as described in REF. Fertilized eggs were sampled in a small volume of medium every 40 minutes from fertilization into the cap of an 1.5 ml Eppendorf tube. Excess water was removed using a micro mouthpipette and the embryo flash frozen in liquid nitrogen.", "time min post fertilization:3960", "GSM1483834", "GSM1483834: Metazome ZF timecourse sample 0099; Danio rerio; RNA Seq", "GSM1483834", null, "1", "RNA was isolated using TRIzol as previously described Levin et al.  2012. The CEL Seq protocol Hashimshony  et al. 2012 was used to amplify and sequence. CEL seq multiplexing barocdes were used.", "GEO Accession:GSM1483834", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP045679", null, null, "Metazome_ZF_timecourse_sample_0099.fastq.gz", "fastq", 284196500.0, 8119900.0, "GSM1483834 r1", "0:35", "A:81991733;C:57440756;G:58362818;T:86010858;N:390335", 35, null, null, null, 81991733, 57440756, 58362818, 86010858, 390335, "SRX684699", "SRS687817", "SRA179995", "GEO", "Yanai, Biology, Technion - Israel Institute of Technology", 1, 0.81284, null, 0.1715, null, 0.78468, null, 0.49472, null, 35, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "celseq", null, "Israel", "2014-08-21", "Zygote", "Embryo", "Embryo Imprecise", "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": ["38129"], "units": {}, "query_ms": 10.229955005343072}