run_metadata: 44071

This data as json

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
44071	SRR6246043	SRX3353217	SRS2652437	SRP123447	PRJNA416866	Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits [RNA Seq]	GSE106430	Other	What genomic changes led to the origin of vertebrates remains a mystery. On the one hand animal evolution is thought to be driven mostly by changes in the cis regulatory regions of a shared conserved and toolkit of developmental genes. On the other hand vertebrates experienced two rounds of whole genome duplication WGD that increased their gene repertoire particularly of regulatory genes controlling embryo development. To shed light into the origin and evolution of the vertebrate regulatory genome we have generated an unprecedented transcriptomic and epigenomic resource for the non duplicated genome of the European amphioxus a closely related invertebrate chordate. These data include RNA seq for more than 35 developmental stages and adult tissues CAGE seq ChIP seq bisulphite seq and ATAC seq for several developmental stages and adult tissues. By comparing these data sets with equivalent novel and previously available data for various vertebrate species especially zebrafish we uncovered multiple conserved and vertebrate specific regulatory landmarks. We first identify a conserved chordate phylotypic stage a developmental period in which different chordate species show the highest gene expression similarity. We also shed light on the origin of enhancer demethylation in vertebrates by identifying for the first time in an invertebrate species differentially methylated enhancers. Furthermore we show that conserved clusters of co expressed and tissue specific genes display similar enrichments for cis regulatory motifs between amphioxus and vertebrates. Finally we study the impact of vertebrate WGDs on the evolution of gene regulation providing the first genome wide quantitative assessment of sub functionalization and neo functionalization processes post the vertebrate WGDs; changing the way in which these evolutionary mechanisms have been traditionally understood. Overall design: RNA seq assays in different developmental stages of european amphioxus zebrafish and medaka	parent bioproject:PRJNA416859	pubmed:30464347		RNAseq zebrafish 2 hpf	GSM2837572		tissue:whole embryo\|developmental stage:2 hpf	RNAseq zebrafish 2 hpf	Reads were aligned against reference genome using Tophat2 software and gene models were built using Cufflinks. Genome build: Amphioxus Bl71nemr Genomic sequencing data was submitted to ENA under the master PRJEB13665 accession Zebrafish September 2014 GRCz10/danRer10 Medaka October 2005 oryLat2. Supplementary files format and content: Individual RPKM files reads per kilobase per million mapped reads for amphioxus and zebrafish. Complete table of TPM transcripts per million for medaka.	whole embryo		Embryos were fixed in RNAlater Thermo Fisher Scientific and RNA extracted using RNeasy Mini Kit Qiagen	Embryos were cultivated at 28°C in E3 medium until desired developmental stage	developmental stage:2 hpf	GSM2837572	GSM2837572: RNAseq zebrafish 2 hpf; Danio rerio; RNA Seq	GSM2837572		1	Embryos were fixed in RNAlater Thermo Fisher Scientific and RNA extracted using RNeasy Mini Kit Qiagen	GEO Accession:GSM2837572	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2500		SRP123447			RNAseq_zebra_2hpf_1.fq.gz RNAseq_zebra_2hpf_2.fq.gz	fastq fastq	17109578000.0	68438312.0	GSM2837572 r1	0:125 1:125	A:4536550134;C:4009266695;G:4076560218;T:4484964079;N:2236874	125	125			4536550134	4009266695	4076560218	4484964079	2236874	SRX3353217	SRS2652437	SRA627467	GEO	CABD/CSIC	2	0.9622	0.96459	0.02758	0.02719	0.7713	0.77327	0.48657	0.48547	125	125	B	B	biological fallback assumption	illumina	hiseq_era	unknown	random_priming	unknown	bulk	unknown	unknown		Spain	2017-11-02	Cleavage	Embryo	Whole Organism	All anatomical structures