|
| Status |
Public on May 18, 2015 |
| Title |
morpholino control (miRNA-Seq) |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Danio rerio |
| Characteristics |
genotype: control morpholino
developmental stage: embryo 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.
small RNA libraries were constructed using the Illumina miRNA-Seq library preparation kit according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
FASTX-Toolkit clipper was used to remove sequencing adapters.
The .fastq file was converted to a tab-delimited file which held only the unique sequence read and its corresponding number of copies.
The files were uploaded to DSAP (http://dsap.cgu.edu.tw/index.htm) for clustering of tags, classification of non-coding small RNAs and miRNAs basis on sequencing homology search against the Rfam and miRBase database respectively.
The differential expressed miRNAs were detected by R package DEGseq using the output data of DSAP.
Genome_build: Zv9
|
| |
|
| Submission date |
Jan 21, 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) |
| GSE54259 |
Systematic Transcriptome Analysis of Zebrafish Model of Diamond-Blackfan Anemia from RPS24 Deficiency (miRNA-Seq) |
| GSE54270 |
Systematic Transcriptome Analysis of Zebrafish Model of Diamond-Blackfan Anemia from RPS24 Deficiency |
|
| Relations |
| BioSample |
SAMN02593630 |
| SRA |
SRX445322 |
