|
| Status |
Public on Nov 17, 2011 |
| Title |
shield-3 |
| Sample type |
SRA |
| |
|
| Source name |
Shield RNA-Seq
|
| Organism |
Danio rerio |
| Characteristics |
tissue: embryo
developmental stage: embryogenesis: shield stage
average insert size (fragment length): 301.27025
stdev for insert size: 160.492253
|
| Growth protocol |
Zebrafish embryos were dechorionated at the 1-cell stage, followed by incubation at 28C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using the standard Trizol (Invitrogen) protocol. Two rounds of PolyA+-RNA purification were performed for each sample, using the PolyA(Purist)TM-MAG kit (Ambion). The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bioanalyzer. Strand-specific libraries for 76 bp paired-end sequencing were prepared according to a modified UTP-method (Parkhomchuk et al. 2009), as detailed in (Levin et al. 2010).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA-Seq
|
| Data processing |
Th summary result files of he developmental transcriptome of all samples are available as supplementary information with the paper.
|
| |
|
| Submission date |
Nov 11, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Eivind Valen |
| E-mail(s) |
eivind.valen@gmail.com
|
| Organization name |
University of Copenhagen
|
| Department |
Dep. of Biology
|
| Lab |
Sandelin
|
| Street address |
Ole Maaloes Vej 4
|
| City |
Copenhagen E |
| State/province |
Select |
| ZIP/Postal code |
2100 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL14875 |
| Series (2) |
| GSE32898 |
Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis [RNA_seq] |
| GSE32900 |
Comprehensive identification of long non-coding RNAs expressed during zebrafish embryogenesis |
|
| Relations |
| SRA |
SRX107391 |
| BioSample |
SAMN00760480 |
