|
| Status |
Public on Oct 09, 2013 |
| Title |
RPS19+p53 MO |
| Sample type |
SRA |
| |
|
| Source name |
RPS19+p53 MO_embryo
|
| Organism |
Danio rerio |
| Characteristics |
genotype/variation: RPS19 and p53 morpholino double knockdown
tissue: embryo
age: 48hpf
|
| Treatment protocol |
Zebrafish embryos at the one-cell stage were injected with the MOs using an Microinjector (WPI SYS-PV830). Based on initial injection trials, 2-5 ng MO and control MO was chosen as the optimal concentration.
|
| Growth protocol |
Zebrafish embryos were kept in a 28.5℃ incubator to 48hpf
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Immediately after harvesting, 40-50 pooled embryos at 48 hpf from different experiment replicates were snap-frozen in liquid nitrogen and stored at -80°C. Total RNA was extracted from the pooled embryos using TRIzol (Invitrogen) according to the manufacturer’s instructions.
mRNA libraries were constructed using the Illumina mRNA-Seq library preparation kit according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 3
|
| Data processing |
TopHat for mapping of Hiseq 2000 RNA-Seq data
Cufflinks for assembling transcripts, estimating their abundances, and testing for differential expression and regulation in RNA-Seq samples
Computation and visualization were achieved using the heatmap plus package in R.
IPA and the Gene Ontology for functional analysis of specific genes
Genome_build: Zv9
Supplementary_files_format_and_content: tab-delimited text files include abundance measurements (FPKM values) for each sample
|
| |
|
| Submission date |
Apr 02, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
yadong yang |
| E-mail(s) |
yangyd@big.ac.cn
|
| Organization name |
Beijing Institute of Genomics
|
| Street address |
No.1-104 Beichen West Road, Chaoyang
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL14875 |
| Series (1) |
| GSE45699 |
Transcriptome analysis of the Zebrafish model of Diamond-Blackfan Anemia from RPS19 deficiency via p53-dependent and -independent pathways |
|
| Relations |
| SRA |
SRX258125 |
| BioSample |
SAMN01996002 |
