|
Status |
Public on May 18, 2015 |
Title |
RPS24_MO |
Sample type |
SRA |
|
|
Source name |
embryo
|
Organism |
Danio rerio |
Characteristics |
developmental stage: embryo age: 48hpf genotype/variation: RPS24-deficient
|
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 2
|
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 .txt files report abundance measurements (FPKM).
|
|
|
Submission date |
Jan 16, 2014 |
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 (2) |
GSE54152 |
Systematic Transcriptome Analysis of Zebrafish Model of Diamond-Blackfan Anemia from RPS24 Deficiency (mRNA-Seq) |
GSE54270 |
Systematic Transcriptome Analysis of Zebrafish Model of Diamond-Blackfan Anemia from RPS24 Deficiency |
|
Relations |
BioSample |
SAMN02585413 |
SRA |
SRX435195 |