Series Summary for DCD000170SR

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

Survey

10.1101/gr.116012.110

GSE22830

Maternally deposited mRNAs direct early development before the initiation of zygotic transcription during mid-blastula transition (MBT). To study mechanisms regulating this developmental event in zebrafish, we applied mRNA deep sequencing technology and generated comprehensive information and valuable resources on transcriptome dynamics during early embryonic (egg to early gastrulation) stages. Genome-wide transcriptome analysis documented at least 8000 maternal genes and identified the earliest cohort of zygotic transcripts. We determined expression levels of maternal and zygotic transcripts with the highest resolution possible using mRNA-seq and clustered them based on their expression pattern. We unravel delayed polyadenylation in a large cohort of maternal transcripts prior to the MBT for the first time in zebrafish. Blocking polyadenylation of these transcripts confirms their role in regulating development from the MBT onward. Our study also identified a large number of novel transcribed regions in annotated and unannotated regions of the genome, which will facilitate reannotation of the zebrafish genome. We also identified splice variants with an estimated frequency of 50%–60%.

True

cwinata

May 16, 2016, 7:51 a.m.

Oct. 22, 2018, 9:55 p.m.

Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006314BS DCD000170SR tissue Mathavan Lab, NTU Medical School AB 90 Days-2 Years adult
Applied Assay ID Biosample Replicate Assay
DCD000977AA DCD012442BR RNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Maximum Read Length Sequencing Date
DCD000835SQ DCD000974TR Mathavan Lab, NTU Medical School SOLiD AB SOLiD System forward 01/01/2011
DCD000540DT: FASTQ
DCD003956DT: LOG GRCz10/danRer10
DCD003957DT: TSV GRCz10/danRer10
DCD003958DT: BEDGRAPH GRCz10/danRer10
DCD003960DT: BEDGRAPH GRCz10/danRer10
DCD003962DT: BEDGRAPH GRCz10/danRer10
DCD003963DT: PDF GRCz10/danRer10
DCD003964DT: LOG GRCz10/danRer10
DCD003965DT: PDF GRCz10/danRer10
DCD003966DT: LOG GRCz10/danRer10
DCD003967DT: BEDGRAPH GRCz10/danRer10
DCD003971DT: BEDGRAPH GRCz10/danRer10
DCD004018DT: BAM GRCz10/danRer10
DCD008678DT: BIGWIG GRCz10/danRer10
DCD015104DT: LOG GRCz11/danRer11
DCD015107DT: TSV GRCz11/danRer11
DCD015108DT: TSV GRCz11/danRer11
DCD015109DT: BIGWIG GRCz11/danRer11
DCD015110DT: BEDGRAPH GRCz11/danRer11
DCD015111DT: PDF GRCz11/danRer11
DCD015112DT: LOG GRCz11/danRer11
DCD015113DT: LOG GRCz11/danRer11
DCD015114DT: PDF GRCz11/danRer11
DCD015116DT: BEDGRAPH GRCz11/danRer11
DCD015138DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006315BS DCD000170SR whole organism Mathavan Lab, NTU Medical School AB 1-cell 0
Applied Assay ID Biosample Replicate Assay
DCD000978AA DCD012441BR RNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD000836SQ DCD000975TR Mathavan Lab, NTU Medical School SOLiD AB SOLiD System forward 01/01/2011
DCD000541DT: FASTQ
DCD004052DT: LOG GRCz10/danRer10
DCD004053DT: TSV GRCz10/danRer10
DCD004054DT: BEDGRAPH GRCz10/danRer10
DCD004056DT: BEDGRAPH GRCz10/danRer10
DCD004057DT: BEDGRAPH GRCz10/danRer10
DCD004058DT: BEDGRAPH GRCz10/danRer10
DCD004059DT: PDF GRCz10/danRer10
DCD004060DT: LOG GRCz10/danRer10
DCD004061DT: PDF GRCz10/danRer10
DCD004062DT: LOG GRCz10/danRer10
DCD004065DT: BEDGRAPH GRCz10/danRer10
DCD004114DT: BAM GRCz10/danRer10
DCD008556DT: BIGWIG GRCz10/danRer10
DCD008557DT: BIGWIG GRCz10/danRer10
DCD015115DT: LOG GRCz11/danRer11
DCD015117DT: TSV GRCz11/danRer11
DCD015118DT: TSV GRCz11/danRer11
DCD015119DT: BEDGRAPH GRCz11/danRer11
DCD015120DT: BEDGRAPH GRCz11/danRer11
DCD015121DT: BIGWIG GRCz11/danRer11
DCD015122DT: BIGWIG GRCz11/danRer11
DCD015123DT: PDF GRCz11/danRer11
DCD015124DT: LOG GRCz11/danRer11
DCD015125DT: LOG GRCz11/danRer11
DCD015126DT: PDF GRCz11/danRer11
DCD015129DT: BEDGRAPH GRCz11/danRer11
DCD015131DT: BEDGRAPH GRCz11/danRer11
DCD015143DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006316BS DCD000170SR whole organism Mathavan Lab, NTU Medical School AB 16-cell 1.5
Applied Assay ID Biosample Replicate Assay
DCD000979AA DCD012440BR RNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD000837SQ DCD000976TR Mathavan Lab, NTU Medical School SOLiD AB SOLiD System forward 01/01/2011
DCD000542DT: FASTQ
DCD003920DT: LOG GRCz10/danRer10
DCD003921DT: TSV GRCz10/danRer10
DCD003922DT: BEDGRAPH GRCz10/danRer10
DCD003923DT: BEDGRAPH GRCz10/danRer10
DCD003925DT: BEDGRAPH GRCz10/danRer10
DCD003927DT: PDF GRCz10/danRer10
DCD003928DT: BEDGRAPH GRCz10/danRer10
DCD003929DT: LOG GRCz10/danRer10
DCD003930DT: PDF GRCz10/danRer10
DCD003931DT: LOG GRCz10/danRer10
DCD003936DT: BEDGRAPH GRCz10/danRer10
DCD003983DT: BAM GRCz10/danRer10
DCD008680DT: BIGWIG GRCz10/danRer10
DCD015127DT: LOG GRCz11/danRer11
DCD015128DT: TSV GRCz11/danRer11
DCD015130DT: TSV GRCz11/danRer11
DCD015132DT: BIGWIG GRCz11/danRer11
DCD015133DT: PDF GRCz11/danRer11
DCD015134DT: BEDGRAPH GRCz11/danRer11
DCD015135DT: LOG GRCz11/danRer11
DCD015136DT: PDF GRCz11/danRer11
DCD015137DT: LOG GRCz11/danRer11
DCD015145DT: BEDGRAPH GRCz11/danRer11
DCD015174DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006317BS DCD000170SR whole organism Mathavan Lab, NTU Medical School AB 128-cell 2.25
Applied Assay ID Biosample Replicate Assay
DCD000980AA DCD012439BR RNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD000838SQ DCD000977TR Mathavan Lab, NTU Medical School SOLiD AB SOLiD System forward 01/01/2011
DCD000543DT: FASTQ
DCD003968DT: LOG GRCz10/danRer10
DCD003969DT: TSV GRCz10/danRer10
DCD003970DT: BEDGRAPH GRCz10/danRer10
DCD003972DT: BEDGRAPH GRCz10/danRer10
DCD003973DT: BEDGRAPH GRCz10/danRer10
DCD003974DT: BEDGRAPH GRCz10/danRer10
DCD003975DT: PDF GRCz10/danRer10
DCD003976DT: LOG GRCz10/danRer10
DCD003977DT: PDF GRCz10/danRer10
DCD003978DT: LOG GRCz10/danRer10
DCD003979DT: BEDGRAPH GRCz10/danRer10
DCD004063DT: BAM GRCz10/danRer10
DCD008544DT: BIGWIG GRCz10/danRer10
DCD008545DT: BIGWIG GRCz10/danRer10
DCD015139DT: LOG GRCz11/danRer11
DCD015140DT: TSV GRCz11/danRer11
DCD015141DT: TSV GRCz11/danRer11
DCD015142DT: BEDGRAPH GRCz11/danRer11
DCD015144DT: BEDGRAPH GRCz11/danRer11
DCD015146DT: BEDGRAPH GRCz11/danRer11
DCD015147DT: BIGWIG GRCz11/danRer11
DCD015148DT: PDF GRCz11/danRer11
DCD015149DT: BIGWIG GRCz11/danRer11
DCD015150DT: LOG GRCz11/danRer11
DCD015151DT: PDF GRCz11/danRer11
DCD015152DT: LOG GRCz11/danRer11
DCD015156DT: BEDGRAPH GRCz11/danRer11
DCD015170DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006318BS DCD000170SR whole organism Mathavan Lab, NTU Medical School AB High 3.5
Applied Assay ID Biosample Replicate Assay
DCD000981AA DCD012438BR RNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD000839SQ DCD000978TR Mathavan Lab, NTU Medical School SOLiD AB SOLiD System forward 01/01/2011
DCD000544DT: FASTQ
DCD003884DT: LOG GRCz10/danRer10
DCD003885DT: TSV GRCz10/danRer10
DCD003886DT: BEDGRAPH GRCz10/danRer10
DCD003888DT: BEDGRAPH GRCz10/danRer10
DCD003890DT: BEDGRAPH GRCz10/danRer10
DCD003891DT: PDF GRCz10/danRer10
DCD003892DT: LOG GRCz10/danRer10
DCD003893DT: PDF GRCz10/danRer10
DCD003894DT: LOG GRCz10/danRer10
DCD003899DT: BEDGRAPH GRCz10/danRer10
DCD003900DT: BEDGRAPH GRCz10/danRer10
DCD003947DT: BAM GRCz10/danRer10
DCD008682DT: BIGWIG GRCz10/danRer10
DCD015153DT: LOG GRCz11/danRer11
DCD015154DT: TSV GRCz11/danRer11
DCD015155DT: TSV GRCz11/danRer11
DCD015157DT: BIGWIG GRCz11/danRer11
DCD015158DT: PDF GRCz11/danRer11
DCD015159DT: LOG GRCz11/danRer11
DCD015160DT: PDF GRCz11/danRer11
DCD015161DT: BEDGRAPH GRCz11/danRer11
DCD015162DT: LOG GRCz11/danRer11
DCD015167DT: BEDGRAPH GRCz11/danRer11
DCD015180DT: BAM GRCz11/danRer11
Biosample ID Series biosample_type biosample_lab genetic_background stage Hours Post Fertilization
DCD006319BS DCD000170SR whole organism Mathavan Lab, NTU Medical School AB 50%-epiboly 5.3
Applied Assay ID Biosample Replicate Assay
DCD000982AA DCD012437BR RNA-seq_Mathavan_Lab_0001AS
Sequencing ID Technical Replicate Sequencing Lab Platform Instrument Strand Sequencing Date
DCD000840SQ DCD000979TR Mathavan Lab, NTU Medical School SOLiD AB SOLiD System forward 01/01/2011
DCD000545DT: FASTQ
DCD003393DT: LOG GRCz10/danRer10
DCD003394DT: TSV GRCz10/danRer10
DCD003395DT: BEDGRAPH GRCz10/danRer10
DCD003396DT: BEDGRAPH GRCz10/danRer10
DCD003397DT: BEDGRAPH GRCz10/danRer10
DCD003398DT: BEDGRAPH GRCz10/danRer10
DCD003399DT: PDF GRCz10/danRer10
DCD003400DT: LOG GRCz10/danRer10
DCD003401DT: PDF GRCz10/danRer10
DCD003402DT: LOG GRCz10/danRer10
DCD003407DT: BEDGRAPH GRCz10/danRer10
DCD003492DT: BAM GRCz10/danRer10
DCD008694DT: BIGWIG GRCz10/danRer10
DCD015163DT: LOG GRCz11/danRer11
DCD015164DT: TSV GRCz11/danRer11
DCD015165DT: TSV GRCz11/danRer11
DCD015166DT: BEDGRAPH GRCz11/danRer11
DCD015168DT: BIGWIG GRCz11/danRer11
DCD015169DT: PDF GRCz11/danRer11
DCD015171DT: LOG GRCz11/danRer11
DCD015172DT: PDF GRCz11/danRer11
DCD015173DT: LOG GRCz11/danRer11
DCD015189DT: BEDGRAPH GRCz11/danRer11
DCD015203DT: BAM GRCz11/danRer11