|
| Status |
Public on Sep 27, 2022 |
| Title |
Subj_3 baseline [S3] |
| Sample type |
SRA |
| |
|
| Source name |
skeletal muscle
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skeletal muscle
subject: Subj_3
treatment: baseline
|
| Extracted molecule |
total RNA |
| Extraction protocol |
In each participant, a vastus lateralis muscle biopsy (∼150 mg) was collected using a Weil–Blakesley conchotome at ∼2 cm from the motor point. Two ml of lidocaine (2%) were injected in the area of the sampling and a small incision of muscle and fascia was performed. Muscle samples were frozen in liquid nitrogen and stored at −80°C. RNA was extracted from the muscle tissues by REPROCELL (USA) using a Norgen Animal Tissue RNA Purification Kit #257 (Norgen Biotek Corp, Ontario, CA).
RNA-Seq was performed at the Frederick National Laboratory for Cancer Research Sequencing Facility, NIH. The libraries were made using the TruSeq Stranded Total RNA Library Prep protocol from Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
31 totalRNA-Seq samples were pooled and sequenced on 2 lanes of a NovaSeq 6000 S4 XP run using Illumina(R) Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and paired-end sequencing.
|
| Data processing |
Reads were trimmed using Cutadapt (v. 1.18) to remove sequencing adapters.
Reads were aligned to human reference genome hg38 using STAR (v. 2.7.0f)
Expression levels were quantified using RSEM (v. 1.3.0) with GENCODE annotation (v. 21)
Assembly: hg38
Supplementary files format and content: RSEM raw counts as tab-delimited file for 58,381 genes (rows) and 31 samples (columns).
|
| |
|
| Submission date |
Aug 15, 2022 |
| Last update date |
Sep 27, 2022 |
| Contact name |
Luigi Ferrucci |
| E-mail(s) |
ferruccilu@grc.nia.nih.gov
|
| Organization name |
National Institute on Aging, National Institutes of Health
|
| Department |
Translational Gerontology Branch
|
| Lab |
Longitudinal Studies Section
|
| Street address |
251 BAYVIEW BLVD.
|
| City |
BALTIMORE |
| State/province |
MD |
| ZIP/Postal code |
21224 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE211204 |
Ten-day human unilateral lower limb suspension and active recovery in young healthy men |
|
| Relations |
| BioSample |
SAMN30311132 |
| SRA |
SRX17065164 |
