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 | Controlled By | anatomical_term | Treatment | Hours Post Fertilization | Mutation Description |
---|---|---|---|---|---|---|---|---|---|---|
DCD006314BS | DCD000170SR | tissue | Mathavan Lab, NTU Medical School | AB | 90 Days-2 Years | unfertilized egg | — | adult | — |
Applied Assay ID | Biosample Replicate | Assay | Controlled By |
---|---|---|---|
DCD000977AA | DCD012442BR | RNA-seq_Mathavan_Lab_0001AS |
Sequencing ID | Technical Replicate | Sequencing Lab | Platform | Instrument | Chemistry Version | Paired End | Strand | Maximum Read Length | Sequencing Date |
---|---|---|---|---|---|---|---|---|---|
DCD000835SQ | DCD000974TR | Mathavan Lab, NTU Medical School | SOLiD | AB SOLiD System | — | ✘ | forward | — | 01/01/2011 |
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 |
Biosample ID | Series | biosample_type | biosample_lab | genetic_background | stage | anatomical_term | 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 |
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 |
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 |
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 |