|
| Status |
Public on Apr 30, 2019 |
| Title |
5mRNA |
| Sample type |
SRA |
| |
|
| Source name |
larvae
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB
age: 6 day post fertilization
treatment: injection atg5 mRNA
genotype: atg5 overexpression
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A total amount of 1.5μ g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to danRer10 whole genome using STAR 2.5.2a
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: danRer10
Supplementary_files_format_and_content: RPKMs
|
| |
|
| Submission date |
Sep 19, 2018 |
| Last update date |
Apr 30, 2019 |
| Contact name |
zhanying hu |
| E-mail(s) |
zhanying.hu@bblumberg.org
|
| Organization name |
Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College
|
| Street address |
1# tiantanxili, dongcheng district
|
| City |
beijing |
| ZIP/Postal code |
100050 |
| Country |
China |
| |
|
| Platform ID |
GPL21741 |
| Series (1) |
| GSE120170 |
Next Generation Sequencing analysis atg5 gene expression in zebrafish model |
|
| Relations |
| BioSample |
SAMN10090354 |
| SRA |
SRX4714814 |
