Series Summary for DCD000328SR

RNA-sequencing project for zebrafish embryo and larva development

Survey

10.1371/journal.pone.0064058

GSE45706

Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. Recent years have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes, yet large gaps still remain in the functional pathways critical for each developmental stage, especially for the late embryonic development. We sequenced the polyA-extracted mRNA from 9 stages covering 7 major developmental periods of zebrafish. Whole genome gene expression pattern were analyzed to reveal unknown pathways or factors with implicated roles during each stage of vertebrate development.

True

mickael.dong

May 9, 2017, 6:59 a.m.

June 8, 2018, 5:29 a.m.

Assays

RNA-seq

Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006908BS DCD000328SR whole organism Yang Lab, Shanghai Chenshan Botanical Garden AB 64-cell 2
Applied Assay ID Biosample Replicate Assay
DCD001897AA DCD013418BR RNA-seq_Yang_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002248SQ DCD002255TR Yang Lab, Shanghai Chenshan Botanical Garden SOLiD AB SOLiD System unstranded 04/30/2013
DCD004719DT: FASTQ
DCD008857DT: BIGWIG GRCz10/danRer10
DCD009155DT: LOG GRCz10/danRer10
DCD009157DT: TSV GRCz10/danRer10
DCD009158DT: TSV GRCz10/danRer10
DCD009159DT: BEDGRAPH GRCz10/danRer10
DCD009160DT: BEDGRAPH GRCz10/danRer10
DCD009161DT: PDF GRCz10/danRer10
DCD009162DT: LOG GRCz10/danRer10
DCD009163DT: PDF GRCz10/danRer10
DCD009164DT: LOG GRCz10/danRer10
DCD009166DT: BEDGRAPH GRCz10/danRer10
DCD009171DT: BEDGRAPH GRCz10/danRer10
DCD009183DT: BAM GRCz10/danRer10
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006909BS DCD000328SR whole organism Yang Lab, Shanghai Chenshan Botanical Garden AB Oblong 3.6
Applied Assay ID Biosample Replicate Assay
DCD001898AA DCD013417BR RNA-seq_Yang_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002249SQ DCD002256TR Yang Lab, Shanghai Chenshan Botanical Garden SOLiD AB SOLiD System unstranded 04/30/2013
DCD004720DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006910BS DCD000328SR whole organism Yang Lab, Shanghai Chenshan Botanical Garden AB 50%-epiboly 5.25
Applied Assay ID Biosample Replicate Assay
DCD001899AA DCD013416BR RNA-seq_Yang_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002250SQ DCD002257TR Yang Lab, Shanghai Chenshan Botanical Garden SOLiD AB SOLiD System unstranded 04/30/2013
DCD004721DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006911BS DCD000328SR whole organism Yang Lab, Shanghai Chenshan Botanical Garden AB 14-19 somites 16.5
Applied Assay ID Biosample Replicate Assay
DCD001900AA DCD013415BR RNA-seq_Yang_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002251SQ DCD002258TR Yang Lab, Shanghai Chenshan Botanical Garden SOLiD AB SOLiD System unstranded 04/30/2013
DCD004722DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006912BS DCD000328SR whole organism Yang Lab, Shanghai Chenshan Botanical Garden AB Prim-25 36
Applied Assay ID Biosample Replicate Assay
DCD001901AA DCD013414BR RNA-seq_Yang_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002252SQ DCD002259TR Yang Lab, Shanghai Chenshan Botanical Garden SOLiD AB SOLiD System unstranded 04/30/2013
DCD004723DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006913BS DCD000328SR whole organism Yang Lab, Shanghai Chenshan Botanical Garden AB Long-pec 48
Applied Assay ID Biosample Replicate Assay
DCD001902AA DCD013413BR RNA-seq_Yang_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002253SQ DCD002260TR Yang Lab, Shanghai Chenshan Botanical Garden SOLiD AB SOLiD System unstranded 04/30/2013
DCD004724DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006914BS DCD000328SR whole organism Yang Lab, Shanghai Chenshan Botanical Garden AB Pec-fin 60
Applied Assay ID Biosample Replicate Assay
DCD001904AA DCD013411BR RNA-seq_Yang_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002255SQ DCD002262TR Yang Lab, Shanghai Chenshan Botanical Garden SOLiD AB SOLiD System unstranded 04/30/2013
DCD004726DT: FASTQ
DCD008840DT: BIGWIG GRCz10/danRer10
DCD009396DT: LOG GRCz10/danRer10
DCD009398DT: TSV GRCz10/danRer10
DCD009399DT: TSV GRCz10/danRer10
DCD009400DT: BEDGRAPH GRCz10/danRer10
DCD009402DT: BEDGRAPH GRCz10/danRer10
DCD009403DT: PDF GRCz10/danRer10
DCD009404DT: LOG GRCz10/danRer10
DCD009405DT: LOG GRCz10/danRer10
DCD009406DT: PDF GRCz10/danRer10
DCD009411DT: BEDGRAPH GRCz10/danRer10
DCD009423DT: BEDGRAPH GRCz10/danRer10
DCD009470DT: BAM GRCz10/danRer10
Applied Assay ID Biosample Replicate Assay
DCD001903AA DCD013412BR RNA-seq_Yang_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002254SQ DCD002261TR Yang Lab, Shanghai Chenshan Botanical Garden SOLiD AB SOLiD System unstranded 04/30/2013
DCD004725DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006915BS DCD000328SR whole organism Yang Lab, Shanghai Chenshan Botanical Garden AB Protruding-mouth 72
Applied Assay ID Biosample Replicate Assay
DCD001905AA DCD013410BR RNA-seq_Yang_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002256SQ DCD002263TR Yang Lab, Shanghai Chenshan Botanical Garden SOLiD AB SOLiD System unstranded 04/30/2013
DCD004727DT: FASTQ
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006916BS DCD000328SR whole organism Yang Lab, Shanghai Chenshan Botanical Garden AB Days 7-13 adult
Applied Assay ID Biosample Replicate Assay
DCD001906AA DCD013409BR RNA-seq_Yang_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD002257SQ DCD002264TR Yang Lab, Shanghai Chenshan Botanical Garden SOLiD AB SOLiD System unstranded 04/30/2013
DCD004728DT: FASTQ