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| Status |
Public on Nov 16, 2015 |
| Title |
S21_age0.003 |
| Sample type |
SRA |
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| Source name |
Skeletal muscle tissues (vastus lateralis)
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| Organism |
Macaca mulatta |
| Characteristics |
age in years: 0.003
age classification: Young
tissue: skeletal muscle
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| Treatment protocol |
N/A
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| Growth protocol |
Monkeys were housed individually in standard nonhuman primate caging on a 12 h light/12 h dark cycle, at room temperature (25.5 ± 0.5 °C), humidity at 60 ± 20%. Monkeys were monitored minimally 3 times daily by trained animal care staff. All monkeys were given normal diets (TestDiet® #5038 Purina Mills, Richmond, IN) and were fed ad libitum. Skeletal muscle tissues (vastus lateralis) were obtained from young (Y), middle-aged (MA), and old (O) monkeys from an ongoing NIA longitudinal study on dietary manipulation and aging that began in 1987
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissues were homogenized in Trizol (Invitrogen, NY) and used to isolate total RNA according to the manufacturer's protocol. Total RNA (5 μg) was treated with 20 U of RNase R (RNR07250, Epicenter) for 15 min at 37⁰C and the digested RNA was isolated using acidic phenol-chloroform (5:1) and ethanol precipitation. CircRNA sequencing was performed at the Genomics Research Center, University of Rochester; 24 samples (one per monkey) were sequenced initially at a depth of approximately 20 million reads (paired-end), and two samples were subsequently sequenced in-depth (at approximately 100 million reads) to assess sample saturation.
Modified TruSeq RNA. Briefly, quantitation and quality of RNA was determing with NanoDrop and Agilent Bioanalyzer 2100, respectively. PolyA capture with oligo-dT beads was omitted and each library was generated from 40ng RNA input with a fragmentation time of 5 minutes at 94C. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-400bp in size. The amplified libraries were hybridized to the Illumina pair end flow cell and amplified using the cBot
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Circular RNA
RNase R treated total RNA
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| Data processing |
Base-Calling: Illumina-RTA 1.18.54
BCL conversion: BCLtoFastq 1.8.4
Sequenced reads were trimmed for adaptor sequence using cutadapt, and the sequences were aligned to the Macaca mulatta (rheMac2) genome with TopHat2 (v2.0.14) and Bowtie2 (v2.2.4), first for linear RNA, and then by searching for fusion transcripts using the reads which did not align to the linear RNA with default parameters using tophat-fusion.
RNA was assembled into linear transcripts using Cufflinks (v2.2.1) using default parameters (except for assembled transfrags are supported by 5 fragments or more were reported) and was annotated using rheMac2 and Ensembl v78.
The circExplorer program was run with the fusion transcripts obtained from TopHat2 using the annotated combined transcripts obtained from the assembled linear RNA for characterizing and annotating circular RNAs.
Genome_build: rheMac2
Supplementary_files_format_and_content: Tab-delimited text in bed12 format (with additional columns at the end) of circRNA splice sites with number of supporting junctional reads in the read_number column for each sample.
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| Submission date |
Sep 10, 2015 |
| Last update date |
Jun 22, 2020 |
| Contact name |
Supriyo De |
| Organization name |
NIA-IRP, NIH
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| Department |
Laboratory of Genetics and Genomics
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| Lab |
Computational Biology & Genomics Core
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| Street address |
251 Bayview Blvd
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21224 |
| Country |
USA |
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| Platform ID |
GPL19129 |
| Series (1) |
| GSE72879 |
Circular RNAs in monkey muscle: age-dependent changes |
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| Relations |
| BioSample |
SAMN04044607 |
| SRA |
SRX1218583 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1874045_S21_identified_circRNA.txt.gz |
86.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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