Series Summary for DCD000433SR

ATAC-seq (5 stages) and RNA-seq data (11 stages) : Functional genomic and transcriptomic analysis of amphioxus and the origin of vertebrate genomic traits

Survey

10.1038/s41586-018-0734-6

PRJNA416859

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,

True

mickael.dong

Sept. 25, 2018, 7:11 a.m.

Feb. 28, 2019, 1:01 a.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007261BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU 20-25 somites 20
Applied Assay ID Biosample Replicate Assay
DCD002675AA DCD014051BR RNA-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003077SQ DCD003117TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 2500 08/16/2018
DCD011079DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007262BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU Prim-5 26
Applied Assay ID Biosample Replicate Assay
DCD002676AA DCD014049BR RNA-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003081SQ DCD003113TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 2500 08/16/2018
DCD011078DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007263BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU 5-9 somites 12
Applied Assay ID Biosample Replicate Assay
DCD002677AA DCD014043BR RNA-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003095SQ DCD003125TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 2500 08/16/2018
DCD011081DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007264BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU 14-19 somites 16
Applied Assay ID Biosample Replicate Assay
DCD002678AA DCD014045BR RNA-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003083SQ DCD003120TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 2500 08/16/2018
DCD011080DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007265BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU Dome 4.33
Applied Assay ID Biosample Replicate Assay
DCD002679AA DCD014052BR ATAC-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003082SQ DCD003124TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 4000 08/16/2018
DCD011084DT: FASTQ
DCD018730DT: BAM GRCz10/danRer10
DCD018732DT: BIGNARROWPEAK GRCz10/danRer10
DCD018733DT: BIGNARROWPEAK GRCz10/danRer10
DCD018734DT: BIGWIG GRCz10/danRer10
DCD018735DT: BED GRCz10/danRer10
DCD019041DT: BIGNARROWPEAK GRCz11/danRer11
DCD019042DT: BED GRCz11/danRer11
DCD019043DT: BIGNARROWPEAK GRCz11/danRer11
DCD019044DT: BIGWIG GRCz11/danRer11
DCD019045DT: BAM GRCz11/danRer11
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003084SQ DCD003122TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 4000 08/16/2018
DCD011085DT: FASTQ
DCD018736DT: BIGNARROWPEAK GRCz10/danRer10
DCD018737DT: BIGNARROWPEAK GRCz10/danRer10
DCD018738DT: BIGWIG GRCz10/danRer10
DCD018739DT: BED GRCz10/danRer10
DCD018740DT: BAM GRCz10/danRer10
DCD019046DT: BIGNARROWPEAK GRCz11/danRer11
DCD019047DT: BIGNARROWPEAK GRCz11/danRer11
DCD019048DT: BED GRCz11/danRer11
DCD019049DT: BAM GRCz11/danRer11
DCD019052DT: BIGWIG GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007266BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU Shield 6
Applied Assay ID Biosample Replicate Assay
DCD002680AA DCD014048BR ATAC-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003090SQ DCD003118TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 4000 08/16/2018
DCD011083DT: FASTQ
DCD018761DT: BAM GRCz10/danRer10
DCD018762DT: BIGNARROWPEAK GRCz10/danRer10
DCD018763DT: BIGNARROWPEAK GRCz10/danRer10
DCD018764DT: BIGWIG GRCz10/danRer10
DCD018765DT: BED GRCz10/danRer10
DCD019071DT: BIGNARROWPEAK GRCz11/danRer11
DCD019072DT: BIGNARROWPEAK GRCz11/danRer11
DCD019073DT: BIGWIG GRCz11/danRer11
DCD019074DT: BED GRCz11/danRer11
DCD019075DT: BAM GRCz11/danRer11
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003087SQ DCD003109TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 4000 08/16/2018
DCD011082DT: FASTQ
DCD018746DT: BAM GRCz10/danRer10
DCD018747DT: BIGNARROWPEAK GRCz10/danRer10
DCD018748DT: BIGNARROWPEAK GRCz10/danRer10
DCD018749DT: BIGWIG GRCz10/danRer10
DCD018750DT: BED GRCz10/danRer10
DCD019054DT: BIGNARROWPEAK GRCz11/danRer11
DCD019055DT: BIGNARROWPEAK GRCz11/danRer11
DCD019056DT: BED GRCz11/danRer11
DCD019059DT: BAM GRCz11/danRer11
DCD019062DT: BIGWIG GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007267BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU 75%-epiboly 8
Applied Assay ID Biosample Replicate Assay
DCD002681AA DCD014044BR ATAC-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003089SQ DCD003112TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 4000 08/16/2018
DCD011088DT: FASTQ
DCD018755DT: BAM GRCz10/danRer10
DCD018757DT: BIGNARROWPEAK GRCz10/danRer10
DCD018758DT: BIGNARROWPEAK GRCz10/danRer10
DCD018759DT: BIGWIG GRCz10/danRer10
DCD018760DT: BED GRCz10/danRer10
DCD019065DT: BIGNARROWPEAK GRCz11/danRer11
DCD019066DT: BIGNARROWPEAK GRCz11/danRer11
DCD019067DT: BIGWIG GRCz11/danRer11
DCD019068DT: BED GRCz11/danRer11
DCD019069DT: BAM GRCz11/danRer11
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003086SQ DCD003106TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 4000 08/16/2018
DCD011089DT: FASTQ
DCD018741DT: BAM GRCz10/danRer10
DCD018742DT: BIGNARROWPEAK GRCz10/danRer10
DCD018743DT: BIGNARROWPEAK GRCz10/danRer10
DCD018744DT: BIGWIG GRCz10/danRer10
DCD018745DT: BED GRCz10/danRer10
DCD019050DT: BIGNARROWPEAK GRCz11/danRer11
DCD019051DT: BIGNARROWPEAK GRCz11/danRer11
DCD019053DT: BED GRCz11/danRer11
DCD019057DT: BIGWIG GRCz11/danRer11
DCD019058DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007268BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU 5-9 somites 12
Applied Assay ID Biosample Replicate Assay
DCD002682AA DCD014054BR ATAC-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003096SQ DCD003116TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 4000 08/16/2018
DCD011087DT: FASTQ
DCD018771DT: BAM GRCz10/danRer10
DCD018772DT: BIGNARROWPEAK GRCz10/danRer10
DCD018773DT: BIGNARROWPEAK GRCz10/danRer10
DCD018774DT: BIGWIG GRCz10/danRer10
DCD018775DT: BED GRCz10/danRer10
DCD019081DT: BIGNARROWPEAK GRCz11/danRer11
DCD019082DT: BIGNARROWPEAK GRCz11/danRer11
DCD019083DT: BIGWIG GRCz11/danRer11
DCD019084DT: BED GRCz11/danRer11
DCD019090DT: BAM GRCz11/danRer11
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003092SQ DCD003115TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 4000 08/16/2018
DCD011086DT: FASTQ
DCD018766DT: BIGNARROWPEAK GRCz10/danRer10
DCD018767DT: BIGNARROWPEAK GRCz10/danRer10
DCD018768DT: BIGWIG GRCz10/danRer10
DCD018769DT: BED GRCz10/danRer10
DCD018770DT: BAM GRCz10/danRer10
DCD019076DT: BAM GRCz11/danRer11
DCD019077DT: BIGNARROWPEAK GRCz11/danRer11
DCD019078DT: BIGNARROWPEAK GRCz11/danRer11
DCD019079DT: BIGWIG GRCz11/danRer11
DCD019080DT: BED GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007269BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU Long-pec 48
Applied Assay ID Biosample Replicate Assay
DCD002683AA DCD014055BR ATAC-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003088SQ DCD003111TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 4000 08/16/2018
DCD011090DT: FASTQ
DCD018751DT: BIGNARROWPEAK GRCz10/danRer10
DCD018752DT: BIGNARROWPEAK GRCz10/danRer10
DCD018753DT: BIGWIG GRCz10/danRer10
DCD018754DT: BED GRCz10/danRer10
DCD018756DT: BAM GRCz10/danRer10
DCD019060DT: BIGNARROWPEAK GRCz11/danRer11
DCD019061DT: BIGNARROWPEAK GRCz11/danRer11
DCD019063DT: BIGWIG GRCz11/danRer11
DCD019064DT: BED GRCz11/danRer11
DCD019070DT: BAM GRCz11/danRer11
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003079SQ DCD003110TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 4000 08/16/2018
DCD011091DT: FASTQ
DCD018726DT: BIGNARROWPEAK GRCz10/danRer10
DCD018727DT: BIGNARROWPEAK GRCz10/danRer10
DCD018728DT: BIGWIG GRCz10/danRer10
DCD018729DT: BED GRCz10/danRer10
DCD018731DT: BAM GRCz10/danRer10
DCD019036DT: BIGNARROWPEAK GRCz11/danRer11
DCD019037DT: BIGNARROWPEAK GRCz11/danRer11
DCD019038DT: BED GRCz11/danRer11
DCD019039DT: BAM GRCz11/danRer11
DCD019040DT: BIGWIG GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007270BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU 75%-epiboly 8
Applied Assay ID Biosample Replicate Assay
DCD002684AA DCD014057BR RNA-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003080SQ DCD003114TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 2500 08/16/2018
DCD011071DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007271BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU Shield 6
Applied Assay ID Biosample Replicate Assay
DCD002685AA DCD014046BR RNA-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003076SQ DCD003123TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 2500 08/16/2018
DCD011073DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007272BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU Protruding-mouth 72
Applied Assay ID Biosample Replicate Assay
DCD002686AA DCD014056BR RNA-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003085SQ DCD003121TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 2500 08/16/2018
DCD011072DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007273BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU Prim-25 36
Applied Assay ID Biosample Replicate Assay
DCD002687AA DCD014047BR RNA-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003091SQ DCD003119TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 2500 08/16/2018
DCD011075DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007274BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU Long-pec 48
Applied Assay ID Biosample Replicate Assay
DCD002688AA DCD014058BR RNA-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003094SQ DCD003107TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 2500 08/16/2018
DCD011074DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007275BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU 64-cell 2
Applied Assay ID Biosample Replicate Assay
DCD002689AA DCD014050BR RNA-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003078SQ DCD003126TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 2500 08/16/2018
DCD011077DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD007276BS DCD000433SR whole organism Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo AB/TU Prim-15 30
Applied Assay ID Biosample Replicate Assay
DCD002690AA DCD014053BR RNA-seq_Skarmeta_Lab_0002AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Sequencing Date
DCD003093SQ DCD003108TR Skarmeta Lab, Centro Andaluz de Biologia del Desarrollo Illumina HiSeq 2500 08/16/2018
DCD011076DT: FASTQ