Help Login Create account

Data released on March 21, 2018

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

Hwang, Y, S; Seo, M; Choi, H, J; Kim, S, K; Kim, H; Han, J, Y (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 RIS BibTeX Text

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.

Contact Submitter

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

Keywords:

rna-seq single embryonic sequencing single cell sequencing early embryo chicken 

Transcriptomic

http://gigadb.org/images/data/cropped/100418.jpg

Funding:

  • Funding body - National Research Foundation of Korea
  • Award ID - 2015R1A3A2033826
  • Awardee - Jae Yong Han

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

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
...
+
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
...
+
Displaying 1-10 of 30 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 
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).

History:

+

Other datasets you might like: