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Sample GSM1462874

Query DataSets for GSM1462874

Status

Public on Dec 16, 2014

Title

DMSO vehicle

Sample type

SRA

Source name

6 dpf larvae, DMSO vehicle

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