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Sample GSM1462875 Query DataSets for GSM1462875
Status Public on Dec 16, 2014
Title 5 μg/l BDE47 treatment
Sample type SRA
 
Source name 6 dpf larvae, 5 μg/l BDE47 treatment
Organism Danio rerio
Characteristics strain: Tuebingen
tissue: whole larvae
age: 6 day post fertilization
Extracted molecule total RNA
Extraction protocol Zebrafish larvae were homogenized, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina Casava1.7 software used for basecalling.
After obtained from the raw sequencing data, clean reads were mapped into reference zebrafish genome Zv9 assembly, and also H.sapiens hg19 assembly using BLAST to increase the subsequent annotation efficiency.
Trimmed mean of M-values of library size (TMM) 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: zv9
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each Sample
 
Submission date Jul 31, 2014
Last update date May 15, 2019
Contact name Ting Xu
E-mail(s) 412_xuting@tongji.edu.cn
Organization name Tongji University
Street address No. 1239 Road Siping
City Shanghai
ZIP/Postal code 200092
Country China
 
Platform ID GPL14875
Series (1)
GSE59968 Next Generation Sequencing (NGS) of zebrafish larvae transcriptome by 2,2',4,4'-tetrabromodiphenyl ether (BDE47) treatment
Relations
BioSample SAMN02948099
SRA SRX667855

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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