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Data released on February 01, 2018

Supporting data for "The developmental transcriptome atlas of the spoon worm Urechis unicinctus (Echiurida: Annelida)"

Park, C; Han, Y; Lee, S; Ryu, K; Oh, J; A. Kern, E, M; Park, J; Cho, S (2018): Supporting data for "The developmental transcriptome atlas of the spoon worm Urechis unicinctus (Echiurida: Annelida)" GigaScience Database. http://dx.doi.org/10.5524/100393 RIS BibTeX Text

Echiurida is one of the most intriguing major subgroups of the phylum Annelida, because unlike most other annelids, echiurids lack metameric body segmentation as adults. For this reason, transcriptome analyses from various developmental stages of Echiurid can be of substantial value for understanding precise expression levels and the complex regulatory networks during early and larval development. A total of 914 million raw RNA-Seq reads were produced from 14 developmental stages of Urechis unicinctus, and were de novo assembled into contigs spanning 63,928,225 bp with an N50 length of 2,700 bp. The resulting comprehensive transcriptome database of the early developmental stages of U. unicinctus consists of 20,305 representative functional protein-coding transcripts. Approximately 66 % of unigenes were assigned to superphylum-level taxa, including Lophotrochozoa (40%). The completeness of the transcriptome assembly was assessed using BUSCO, and 75.7 % of the metazoan single-copy orthologs were presented in our transcriptome database. We observed three distinct patterns of global transcriptome profiles from 14 developmental stages, and identified a total of 12,705 genes that showed dynamic regulation patterns during the differentiation and maturation of U. unicinctus cells. We present the first large-scale developmental transcriptome dataset of U. unicinctus and provide a general overview of the dynamics of global gene expression changes during its early developmental stages. The analysis of time-course gene expression data is a first step toward understanding the complex developmental gene regulatory networks in U. unicinctus, and will furnish a valuable resource for analyzing the functions of gene repertoires in various developmental phases.

Contact Submitter

Accessions (data included in GigaDB):

PROJECT: PRJNA394029

Keywords:

urechis unicinctus echiurida developmental transcriptome rna-seq de novo assembly 

Transcriptomic

http://gigadb.org/images/data/cropped/100393.jpg

Funding:

  • Funding body - Ministry of Oceans and Fisheries
  • Funding body - National Research Foundation of Korea
  • Award ID - NRF-2016R1D1A1B03933412

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Urechis unicinctus, adult female6432  Urechis unicinctus Life stage:adult
Geographic location (country and/or sea,region):So...
Environment (biome):estuarine mud [ENVO:00002160]
...
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Urechis unicinctus, adult male6432  Urechis unicinctus Life stage:adult
Geographic location (country and/or sea,region):So...
Environment (biome):estuarine mud [ENVO:00002160]
...
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Urechis unicinctus, oocyte6432  Urechis unicinctus Description:Oocyte RNA extracted from embryo of wi...
Life stage:egg
Geographic location (country and/or sea,region):So...
...
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Urechis unicinctus, fertilized_embryo6432  Urechis unicinctus Description:Fertilized embryo RNA extracted from e...
Life stage:embryo
Geographic location (country and/or sea,region):So...
...
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Urechis unicinctus, polar_body6432  Urechis unicinctus Description:Polar body RNA extracted from embryo o...
Life stage:embryo
Geographic location (country and/or sea,region):So...
...
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Urechis unicinctus,2_cell6432  Urechis unicinctus Description:2 cell RNA extracted from embryo of wi...
Life stage:embryo
Geographic location (country and/or sea,region):So...
...
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Urechis unicinctus,4_cell6432  Urechis unicinctus Description:4 cell RNA extracted from embryo of wi...
Life stage:embryo
Geographic location (country and/or sea,region):So...
...
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Urechis unicinctus,8_cell6432  Urechis unicinctus Description:8 cell RNA extracted from embryo of wi...
Life stage:embryo
Geographic location (country and/or sea,region):So...
...
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Urechis unicinctus,16_cell6432  Urechis unicinctus Description:16 cell RNA extracted from embryo of w...
Life stage:embryo
Geographic location (country and/or sea,region):So...
...
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Urechis unicinctus,32_cell6432  Urechis unicinctus Description:32 cell RNA extracted from embryo of w...
Life stage:embryo
Geographic location (country and/or sea,region):So...
...
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Displaying 1-10 of 16 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
ReadmeTEXT4 KB2018-01-30
annotationarchive496.34 KB2018-01-30
annotationarchive1.43 MB2018-01-30
Coding SequenceFASTA27.92 MB2018-01-30
Expression dataUNKNOWN1.89 MB2018-01-31
AnnotationUNKNOWN23.89 MB2018-01-31
Transcriptome sequenceFASTA45.91 MB2018-01-31
protein sequenceFASTA10.22 MB2018-01-30
Phylogenetic treeUNKNOWN0.44 KB2018-01-31
Transcriptome sequenceFASTA531.64 MB2018-01-31
Displaying 1-10 of 13 File(s).

History:

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