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Sample GSM2068003 Query DataSets for GSM2068003
Status Public on Mar 07, 2018
Title Young2
Sample type SRA
 
Source name muscle
Organism Mus musculus
Characteristics strain: C57BL/6
tissue: muscle
age: 3 month
Extracted molecule total RNA
Extraction protocol Muscles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug 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 3000
 
Data processing Illumina HiSeq 3000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using using Tophat2 (version 2.0.10) with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol 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.
Differentially expressed genes were detected using Cuffdiff (version 2.1.1) against RefSeq genes
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date Feb 22, 2016
Last update date May 15, 2019
Contact name Jie Yin
E-mail(s) yinjie@sibcb.ac.cn
Organization name Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
Street address 320 Yueyang Road
City Shanghai
ZIP/Postal code 200031
Country China
 
Platform ID GPL21493
Series (1)
GSE78147 Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type Young and Old muscle Transcriptomes
Relations
BioSample SAMN04505999
SRA SRX1595814

Supplementary file Size Download File type/resource
GSM2068003_young2.txt.gz 403.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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