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| Status |
Public on Mar 07, 2018 |
| Title |
Old2 |
| Sample type |
SRA |
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| Source name |
muscle
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: muscle
age: 20 month
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| 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
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| Submission date |
Feb 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jie Yin |
| E-mail(s) |
yinjie@sibcb.ac.cn
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| Organization name |
Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
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| Street address |
320 Yueyang Road
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| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE78147 |
Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type Young and Old muscle Transcriptomes |
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| Relations |
| BioSample |
SAMN04505997 |
| SRA |
SRX1595812 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2068001_old2.txt.gz |
395.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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