|
Status |
Public on Apr 30, 2019 |
Title |
5MO |
Sample type |
SRA |
|
|
Source name |
larvae
|
Organism |
Danio rerio |
Characteristics |
strain: AB age: 6 day post fertilization treatment: injection 5MO genotype: atg5 knockdown
|
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 |
SAMN10090355 |
SRA |
SRX4714813 |