|
| Status |
Public on Oct 01, 2013 |
| Title |
MO_impdh1b |
| Sample type |
SRA |
| |
|
| Source name |
larvae
|
| Organism |
Danio rerio |
| Characteristics |
treatment: MO impdh1b
strain: AB strain
developmental stage: 32hpf
tissues: whole embryo
|
| Treatment protocol |
The larvae in each group were sucked into freezing tubes, removed of water, frozen immediately in liquid nitrogen, and stored at -80°C.
|
| Growth protocol |
WT larvae, control and impdh knock-down larvae were raised raised at 28°C under 14h: 10h light/dark cycle from birth and sampled simultaneously at 32 hpf.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of each sample was extracted using Trizol (Invitrogen).The quantity and quality of the RNA samples were assessed with a Qbit and an Agilent 2100 bioanalyzer.
mRNA-seq libraries were constructed using the TruSeq RNA Sample Preparation v2 Kit following the manufacturer's protocol (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw sequence reads were mapped to the Danio rerio genome (Danio rerio Zv9), using TopHat (ver. 2.0.9) and gene transfer format (gtf) data (ref_Zv9_scaffolds.gff3.gz from ncbi).
Normalized transcription profiles were estimated based on the mapping results using cufflinks. For each transcript, the number of fragments per kilobase of transcript per million fragments mapped (FPKM) was converted from the raw read counts.
Genome_build: Danio rerio Zv9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample from cufflinks output.
|
| |
|
| Submission date |
Sep 30, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Guang Li |
| E-mail(s) |
liguang@picb.ac.cn
|
| Phone |
0086-021-54920488
|
| Organization name |
PICB
|
| Street address |
320 Yueyang Lu
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL14875 |
| Series (2) |
| GSE51278 |
De Novo Purine Synthesis Mediates Circadian Control of Cell Cycle in Zebrafish (HTS) |
| GSE51279 |
De Novo Purine Synthesis Mediates Circadian Control of Cell Cycle in Zebrafish |
|
| Relations |
| BioSample |
SAMN02369769 |
| SRA |
SRX361626 |
