Illumina HiSeq 2500 sequencing; GSM3003617: Single cell 1 4-cell embryo 1; Ciona intestinalis; RNA-Seq

Single cell 1 4-cell embryo 1

This dataset provides gene expression levels of single cell and pooled embryos as part of a study on zygotic genome activation in Ciona embryogenesis. The single cell RNA-seq data suggested that Cyclin B3 was a key mediator of this process. This was confirmed by performing RNA-seq on pooled RNA isolated from embryos where Cyclin B3 was knocked down (using morpholinos) or overexpressed (using mRNA injections). Overall design: 93 single cell transcriptomes consisting of cells from 4-, 8-, and 16-cell stage embryos. Each stage was performed in triplicate. 21 pooled embryo transcriptomes from total RNA of pooled embryos from 4- 8- and 16-cell stages for controls and embryos where Cyclin B3 has been knocked down (using morpholinos) as well as 16-cell embryos where Cyclin B3 has been overexpressed. All samples were performed in triplicate.

Single cell and pooled embryo RNA-seq of of early Ciona embryos

Submitted by Gene Expression Omnibus on 07-JUL-2018

For single cells, cDNA was prepared directly from cell lysate. For pooled embryos total RNA was purified using Trizol. cDNA was synthesized and amplified from the poly-A containing RNA transcripts in the single-cell lysate using the Smart-Seq2 method. cDNA from cells at 4-cell stage was amplified by 15 cycles of PCR, while 16 cycles of PCR was applied on the cDNA from cells of 8-cell and 16-cell stage embryos.Â The amplified cDNA samples were cleaned up with Ampure XP beads (Beckman Coulter, CA, USA), quantified by Qubit fluorometer (Invitrogen, CA, USA), and examined on Bioanalyzer with High Sensitivity DNA chips (Agilent, CA, USA) for size distribution. Nextera DNA library prep kit (Illumina, CA, USA) was used to convert the cDNA samples to Illumina sequencing libraries. For pooled embryo samples, cDNA synthesis and sequencing was performed as described for single-cells with the exception that 12 cycles of PCR were performed.

Single cell and pooled embryo RNA-seq of of early Ciona embryos

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