Supporting data for "The first whole transcriptomic exploration of pre-oviposited early chicken embryos using single and bulked embryonic RNA-sequencing".

Dataset type: Transcriptomic
Data released on March 21, 2018

Hwang YS; Seo M; Choi HJ; Kim SK; Kim H; Han JY (2018): Supporting data for "The first whole transcriptomic exploration of pre-oviposited early chicken embryos using single and bulked embryonic RNA-sequencing". GigaScience Database. http://dx.doi.org/10.5524/100418

DOI10.5524/100418

The chicken is a valuable model organism, especially in evolutionary and embryology research because its embryonic development occurs in the egg. However, despite its scientific importance, no transcriptome data have been generated for deciphering the early developmental stages of the chicken because of practical and technical constraints accessing pre-oviposited embryos.
Here, we determine the entire transcriptome of pre-oviposited avian embryos, including oocyte, zygote, and intrauterine embryos from Eyal-giladi and Kochav stage I (EGK.I) to EGK.X collected using a non-invasive approach for the first time. We also compare RNA sequencing data obtained using bulked embryo sequencing and single embryo/cell sequencing technique. The raw sequencing data were pre-processed with two different genome builds, Galgal4 and Galgal5, and the expression of 17,108 and 26,102 genes was quantified in the respective builds. There were some differences between the two techniques,as well as between the two genome builds, and these were affected by the emergence of long intergenic non-coding RNA annotations.
The first transcriptome datasets of pre-oviposited early chicken embryos based on bulked and single embryo sequencing techniques will serve as a valuable resource for investigating early avian embryogenesis, for comparative studies among vertebrates, and for novel gene annotation in the chicken genome.

Additional details

Read the peer-reviewed publication(s):

Hwang, Y. S., Seo, M., Bang, S., Kim, H., & Han, J. Y. (2018). Transcriptional and translational dynamics during maternal-to-zygotic transition in early chicken development. The FASEB Journal, 32(4), 2004–2011. doi:10.1096/fj.201700955r (PubMed: 29212819)
Hwang, Y. S., Seo, M., Lee, B. R., Lee, H. J., Park, Y. H., Kim, S. K., … Han, J. Y. (2018). The transcriptome of early chicken embryos reveals signaling pathways governing rapid asymmetric cellularization and lineage segregation. Development, 145(6), dev157453. doi:10.1242/dev.157453 (PubMed: 29467246)

Accessions (data included in GigaDB):

GEO: GSE100798
GEO: GSE86592
PROJECT: PRJNA393103
PROJECT: PRJNA342320





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
EGKIII_S39031ChickenGallus gallus Description:whole RNA extracted from chicken early...
Analyte type:RNA
Alternative accession-SRA Sample:SRS1679748
...
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EGKIII_S49031ChickenGallus gallus Description:whole RNA extracted from chicken early...
Analyte type:RNA
Alternative accession-SRA Sample:SRS1679749
...
+
EGKIII_S59031ChickenGallus gallus Description:whole RNA extracted from chicken early...
Analyte type:RNA
Alternative accession-SRA Sample:SRS1679751
...
+
EGKI_S19031ChickenGallus gallus Description:whole RNA extracted from chicken early...
Analyte type:RNA
Alternative accession-SRA Sample:SRS1679745
...
+
EGKI_S29031ChickenGallus gallus Description:whole RNA extracted from chicken early...
Analyte type:RNA
Alternative accession-SRA Sample:SRS1679746
...
+
EGKI_S49031ChickenGallus gallus Description:whole RNA extracted from chicken early...
Analyte type:RNA
Alternative accession-SRA Sample:SRS1679747
...
+
EGKVIII_S29031ChickenGallus gallus Description:whole RNA extracted from chicken early...
Analyte type:RNA
Alternative accession-SRA Sample:SRS1679754
...
+
EGKVIII_S39031ChickenGallus gallus Description:whole RNA extracted from chicken early...
Analyte type:RNA
Alternative accession-SRA Sample:SRS1679755
...
+
EGKVIII_S49031ChickenGallus gallus Description:whole RNA extracted from chicken early...
Analyte type:RNA
Alternative accession-SRA Sample:SRS1679756
...
+
EGKVI_S19031ChickenGallus gallus Description:whole RNA extracted from chicken early...
Analyte type:RNA
Alternative accession-SRA Sample:SRS1679750
...
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Displaying 1-10 of 30 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
archivearchive48.17 MB2018-02-28
imageTIF36.39 MB2018-02-28
imageTIF36.39 MB2018-02-28
imageTIF36.39 MB2018-02-28
scriptR8.53 KB2018-02-28
annotationTEXT1019.19 KB2018-02-28
annotationTEXT1.46 MB2018-02-28
scriptTEXT1.85 KB2018-02-28
scriptTEXT1.85 KB2018-02-28
imageTIF36.39 MB2018-02-28
Displaying 1-10 of 20 File(s).
Funding body Awardee Award ID Comments
National Research Foundation of Korea Jae Yong Han 2015R1A3A2033826
Date Action
March 21, 2018 Dataset publish