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Sample GSM3395205 Query DataSets for GSM3395205
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

Supplementary file Size Download File type/resource
GSM3395205_5MO_Log.final.out.txt.gz 599 b (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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