|
Status |
Public on Oct 15, 2014 |
Title |
wild-type_AB_sphere_rep1 |
Sample type |
SRA |
|
|
Source name |
whole sphere stage embryo
|
Organism |
Danio rerio |
Characteristics |
genotype: wt developmental stage: Sphere strain: AB
|
Growth protocol |
Embryos were grown in E3 embryo medium at 28.5 degrees celcius
|
Extracted molecule |
polyA RNA |
Extraction protocol |
Total RNA was extracted using Trizol according to manufacturers protocol and treated with Ambion TURBO Dnase. RNA libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
|
Data processing |
Reads were mapped to Zv9 release 68 using Tophat v2.0.5 using the options -p 8 -i 20 -I 380000 --coverage-search --microexon-search Differential expression was determined using Cufflinks with options -p 4 -u Genome_build: Zv9 Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each condition, and statistics for differential expression
|
|
|
Submission date |
Oct 30, 2013 |
Last update date |
May 15, 2019 |
Contact name |
Andrew Christopher Nelson |
E-mail(s) |
a.nelson.1@warwick.ac.uk
|
Organization name |
University of Warwick
|
Department |
School of Life Sciences
|
Street address |
Gibbet Hill Campus
|
City |
Coventry |
ZIP/Postal code |
CV4 7AL |
Country |
United Kingdom |
|
|
Platform ID |
GPL14875 |
Series (2) |
GSE51893 |
Identification of genes differentially expressed in MZeomesa embryos compared with wild-type |
GSE51894 |
Smad2 and Eomesa |
|
Relations |
BioSample |
SAMN02389002 |
SRA |
SRX370992 |