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SRX10386355: GSM5184288: Total RNA (6 hpf); Strongylocentrotus purpuratus; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2000) run: 104.7M spots, 7.9G bases, 3Gb downloads

Submitted by: NCBI (GEO)
Study: Global patterns of enhancer activity during sea urchin embryogenesis assessed by eRNA profiling
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We used CAGE-seq (Capped Analysis of Gene Expression with Sequencing) to profile eRNA expression and enhancer activity during embryogenesis of the sea urchin, Strongylocentrotus purpuratus. We identified >18,000 enhancers that were active during late oogenesis and early development and documented a burst of enhancer activation during cleavage and early blastula stages. Most enhancers were located near gene bodies and eRNA expression levels were highest for elements near core promoters. Transcriptional signals from enhancers generally paralleled the expression levels of likely target genes. Furthermore, enhancers near lineage-specific genes contained signatures of inputs from developmental gene regulatory networks deployed in those lineages. A large fraction (60%) of sea urchin enhancers previously shown to be active in transgenic reporter assays were associated with eRNA expression. Moreover, a large fraction (50%) of a representative subset of enhancers identified by eRNA profiling drove tissue-specific gene expression in isolation when tested by reporter assays. Our findings provide an atlas of developmental enhancers in a model sea urchin and support the utility of eRNA profiling as a tool for enhancer discovery and regulatory biology. The data generated in this study are publicly available at Echinobase ( Overall design: CAGE library preparation, sequencing, mapping, and eRNA identification were performed by DNAFORM (Yokohama, Kanagawa, Japan). Briefly, 30-60 mg total RNA was used for the generation of each CAGE library (9 total) and libraries were subjected to Illumina HiSeq-based sequencing. Sequence reads (>100 million reads/sample) were subjected to quality control (FastQC), filtered to remove small numbers of rRNA reads, and mapped to the S. purpuratus genome (v. 3.1) first with BWA (Li and Durbin, 2010) and then using HISAT2 (Kim et al., 2019) to align reads with BWA MAPQ<20. A total of 60-80 million uniquely mapped reads were obtained per sample and used for all subsequent analysis. De novo eRNA peak-calling was carried out as described by Hirabayashi et al., 2019. Briefly, bidirectional enhancers were identified using the FANTOM5 pipeline (FANTOM CONSRTIUM, 2014). TSSs were identified according to and clustered using the decomposition-based peak identification (DPI) software ( DPI was used with default parameters but without the decomposition parameter. Peaks with at least two supporting CAGE tags were retained and used as input to call bidirectional enhancers using a program available at
Sample: Total RNA (6 hpf)
SAMN18373459 • SRS8509486 • All experiments • All runs
Instrument: Illumina HiSeq 2000
Strategy: RNA-Seq
Selection: CAGE
Layout: SINGLE
Construction protocol: Adult S. purpuratus were obtained from Pat Leahy (Caltech). Gametes were collected by intracoelomic injection of 0.5 M KCl. Fertilization and embryo culture were carried out according to Adams et al. (2019). Embryos were cultured at 15° C in 4-liter plastic beakers fitted with battery powered stirrers. Embryos were harvested at 0, 6, 12, 18, 24, 30, 36, 42, and 48 hr post- fertilization (hpf). The 9 samples were derived from two separate embryo cultures. For the 0 hpf time point, embryos were collected immediately after fertilization. Total RNA (75-100 g/sample) was isolated using the RNeasy Plus Mini kit (Qiagen Cat. No. 74134) and the quality of the preparations was confirmed using an RNA TapeStation (Agilent). RNA integrity numbers (RINs) for all samples were 9.8-10.0. RNA samples were stored at -80°C. CAGE library preparation, sequencing, mapping, and eRNA identification were performed by DNAFORM (Yokohama, Kanagawa, Japan)
Experiment attributes:
GEO Accession: GSM5184288
Runs: 1 run, 104.7M spots, 7.9G bases, 3Gb
Run# of Spots# of BasesSizePublished


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