|
| Status |
Public on Apr 07, 2019 |
| Title |
Basal_Late_A |
| Sample type |
SRA |
| |
|
| Source name |
gastrocnemius muscle
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57bl6
time: Late (ZT22)
running protocole: Basal
gender: male
|
| Treatment protocol |
Mice were acclimated to treadmill running (Panlab Harvard Apparatus, Barcelona, Spain) a day prior to the sprint or the endurance exhaustion test: Pre-test: 10 min without movement follows 10 min at 0.1 m/sec with a 0% slope; 0.4mA shock intensity.Sprint cohort: phase I – 5 min at 8 cm/sec with a 0% slope; phase II – increases by 2 cm/sec every min. Mice ran until they reached failure, which was pre-define as 15 shocks per 60 sec or 25 shocks within 90sec or 30 within 120sec. Time to failure was recorded. Endurance cohort: phase I – 5 min at 8 cm/sec with a 0% slope; phase II – increases by 2 cm/sec every min until reaching a final speed of 20cm/sec. Mice fully performed the high intensity protocol, or performed the moderate intensity test for 1 hour, subsequently their Gastrocnemius muscle was dissected and immediately frozen in liquid nitrogen.
|
| Growth protocol |
All animal experiments and procedures were conducted in conformity with the Institutional Animal Care and Use Committee (IACUC) guidelines. Three months old, males wild type mice were used. Mice were kept under 12 h light/dark regimen and fed either ad libitum or exclusively during the dark or light phase as indicated. ZT0 corresponded to lights on and Z12 to lights off in the animal facility.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Gastrocnemius muscles thawed for 1 minute at RT, then transferred to 2 ml TRI-reagent. Tissue was homogenized using disperser (IKA-T18) and then transferred to 1.7 ml tube and stand in RT for 5 minutes. 200 µL chloroform was added to each tissue sample for phase separation. Samples was then centrifuge for 15 minutes at 13,000 rpm at 4?c and transferred to tubes containing 500 µL Isopropanol. The upper phase was then isolated and stand at RT for 15 minutes and later centrifuged at 13,000 RPM at 4?c. Supernatant was removed and samples washed with 1ml of 75% cold EtOH and briefly vortexed. Sampled was then centrifuged for 10 minutes at 8,000 RPM at 4?c, and washed with 1ml of 75% cold EtOH and briefly vortexed. Pellet was dried, and later dissolved in 150 µL UPW. Samples was then incubated at 56 ?c for 10 minutes. RNA concentration was measured using Nanodrop.
The TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA) was used. The libraries were prepared according to the manufacturer’s protocol without further modifications
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were trimmed using cutadapt and mapped to genome mm10 using STAR v2.4.2a with default parameters.
Counting proceeded over genes annotated in Gencode release mm10 using STAR.
Genome_build: mm10.
Supplementary_files_format_and_content: RNA-seq_raw_counts_Exercise_performance_project.csv
Supplementary_files_format_and_content: Raw read count for each gene in each sample
|
| |
|
| Submission date |
Jul 16, 2018 |
| Last update date |
Apr 07, 2019 |
| Contact name |
Jonathan Aryeh Sobel |
| E-mail(s) |
jonathan.sobel@weizmann.ac.il
|
| Phone |
00972587889058
|
| Organization name |
Weizmann Institute of science
|
| Department |
Biomolecular Sciences
|
| Lab |
Asher
|
| Street address |
Benoziyo Building for Biological Sciences, room 277S, Weizmann Institute of Science
|
| City |
Rehovot |
| ZIP/Postal code |
7610001 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE117161 |
Physiological and molecular dissection of daily variance in exercise capacity |
|
| Relations |
| BioSample |
SAMN09665573 |
| SRA |
SRX4394264 |
