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| Status |
Public on Feb 01, 2020 |
| Title |
1C |
| Sample type |
SRA |
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| Source name |
vastus lateralis muscle
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| Organism |
Homo sapiens |
| Characteristics |
fiber-type: Type IIa
age: old
training.state: untrained
subjectid: 1
time.point: basal
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| Extracted molecule |
total RNA |
| Extraction protocol |
TriZol extraction (TRI Reagent, Molecular Research Center, Cincinnati, OH)
The SMARTer® Ultra® Low Input RNA kit (Takara, Mountain View, CA) was used to generate cDNA from 9 ng of total RNA. Using the ThruPLEX® DNA-seq kit (Takara), 1-2 ng of double-stranded cDNA was end-repaired and A-tailed to prepare for adaptor ligation. Indexed adaptors were ligated to sample DNA, and the adaptor-ligated DNA library quality was assessed by measuring nanomolar concentration and the fragment size in base pairs. Sequencing was performed on the NextSeq 500 unit (Illumina, San Diego, CA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
OHM_pre_featureCounts.txt
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| Data processing |
Basecalling performed using Illumina RTA v2.
bcl2fastq used to convert BCL files to fastq files
Quality control using FastQC v0.11.05
Quality control using Picard 2.7.1 RNASeqMetrics STRAND_SPECIFICITY=NONE
Reads were aligned using STAR v2.5.2b
Gene counts were quantified using featureCounts v1.5.0 with the following settings: -M --fraction -g gene_id
Genome_build: hg38
Supplementary_files_format_and_content: space-delimited matrix of counts per transcript per sample (rows represent transcripts, columns represent samples). First six columns are transcript information (geneid, chromosome, start, end, strand, length).
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| Submission date |
May 09, 2019 |
| Last update date |
Feb 01, 2020 |
| Contact name |
Aliza Rubenstein |
| Organization name |
Icahn School of Medicine at Mount Sinai
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| Street address |
1 Gustave L. Levy Pl
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| City |
Manhattan |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE130977 |
Isolated fiber-type transcriptional profiles in human skeletal muscle |
| GSE236600 |
Effects of lifelong exercise and age on transcriptome dynamics in MHC I and MHC IIa muscle fibers at baseline and in response to resistance exercise (all samples) |
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| Relations |
| BioSample |
SAMN11613336 |
| SRA |
SRX5813960 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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